Variant report

Variant	rs2046969
Chromosome Location	chr3:195648508-195648509
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SRF	chr3:195648056-195648807	ECC-1	luminal epithelium:	n/a	n/a
2	HA-E2F1	chr3:195648043-195648641	MCF-7	breast:	n/a	n/a
3	BACH1	chr3:195648209-195648609	K562	blood:	n/a	chr3:195648372-195648386
4	SRF	chr3:195648215-195648514	H1-hESC	embryonic stem cell:	n/a	n/a
5	JUND	chr3:195648178-195648571	K562	blood:	n/a	chr3:195648373-195648385 chr3:195648374-195648384 chr3:195648375-195648382 chr3:195648373-195648384 chr3:195648374-195648383 chr3:195648375-195648384 chr3:195648375-195648383
6	TCF12	chr3:195647867-195648982	ECC-1	luminal epithelium:	n/a	n/a
7	JUN	chr3:195648070-195648811	K562	blood:	n/a	chr3:195648373-195648385 chr3:195648374-195648384 chr3:195648375-195648382 chr3:195648374-195648383 chr3:195648375-195648384 chr3:195648375-195648383
8	MAFF	chr3:195648062-195648746	K562	blood:	n/a	chr3:195648372-195648386 chr3:195648373-195648391
9	MAFF	chr3:195648166-195648597	HepG2	liver:	n/a	chr3:195648372-195648386 chr3:195648373-195648391
10	MAFK	chr3:195648167-195648682	IMR90	lung:	n/a	chr3:195648376-195648385 chr3:195648266-195648277 chr3:195648369-195648389 chr3:195648373-195648382 chr3:195648375-195648385 chr3:195648378-195648389 chr3:195648374-195648389 chr3:195648371-195648387 chr3:195648372-195648386
11	IRF1	chr3:195648199-195648698	K562	blood:	n/a	chr3:195648374-195648383 chr3:195648375-195648384
12	IRF1	chr3:195648190-195648562	K562	blood:	n/a	chr3:195648374-195648383 chr3:195648375-195648384
13	JUND	chr3:195648196-195648830	H1-hESC	embryonic stem cell:	n/a	chr3:195648373-195648385 chr3:195648374-195648384 chr3:195648375-195648382 chr3:195648373-195648384 chr3:195648374-195648383 chr3:195648375-195648384 chr3:195648375-195648383
14	JUND	chr3:195648194-195648554	Hela-S3	cervix:	n/a	chr3:195648373-195648385 chr3:195648374-195648384 chr3:195648375-195648382 chr3:195648373-195648384 chr3:195648374-195648383 chr3:195648375-195648384 chr3:195648375-195648383
15	NFYB	chr3:195648182-195648612	K562	blood:	n/a	chr3:195648507-195648522 chr3:195648507-195648522 chr3:195648510-195648520
16	MAFK	chr3:195648031-195648800	H1-hESC	embryonic stem cell:	n/a	chr3:195648376-195648385 chr3:195648266-195648277 chr3:195648369-195648389 chr3:195648373-195648382 chr3:195648375-195648385 chr3:195648378-195648389 chr3:195648374-195648389 chr3:195648371-195648387 chr3:195648372-195648386
17	JUND	chr3:195648191-195648553	HepG2	liver:	n/a	chr3:195648373-195648385 chr3:195648374-195648384 chr3:195648375-195648382 chr3:195648373-195648384 chr3:195648374-195648383 chr3:195648375-195648384 chr3:195648375-195648383
18	MAFK	chr3:195648174-195648589	Hela-S3	cervix:	n/a	chr3:195648376-195648385 chr3:195648266-195648277 chr3:195648369-195648389 chr3:195648373-195648382 chr3:195648375-195648385 chr3:195648378-195648389 chr3:195648374-195648389 chr3:195648371-195648387 chr3:195648372-195648386
19	FOS	chr3:195648262-195648531	MCF10A-Er-Src	breast:	n/a	chr3:195648373-195648385 chr3:195648374-195648384 chr3:195648375-195648382 chr3:195648374-195648383 chr3:195648375-195648384 chr3:195648375-195648383
20	MAFK	chr3:195648064-195648766	GM12878	blood:	n/a	chr3:195648376-195648385 chr3:195648266-195648277 chr3:195648369-195648389 chr3:195648373-195648382 chr3:195648375-195648385 chr3:195648378-195648389 chr3:195648374-195648389 chr3:195648371-195648387 chr3:195648372-195648386
21	JUN	chr3:195648192-195648521	HUVEC	blood vessel:	n/a	chr3:195648373-195648385 chr3:195648374-195648384 chr3:195648375-195648382 chr3:195648374-195648383 chr3:195648375-195648384 chr3:195648375-195648383
22	MAFK	chr3:195648186-195648584	HepG2	liver:	n/a	chr3:195648376-195648385 chr3:195648266-195648277 chr3:195648369-195648389 chr3:195648373-195648382 chr3:195648375-195648385 chr3:195648378-195648389 chr3:195648374-195648389 chr3:195648371-195648387 chr3:195648372-195648386
23	MAX	chr3:195647896-195648934	ECC-1	luminal epithelium:	n/a	chr3:195648374-195648383 chr3:195648375-195648384
24	SRF	chr3:195647973-195648815	ECC-1	luminal epithelium:	n/a	n/a
25	NFIC	chr3:195647985-195648950	ECC-1	luminal epithelium:	n/a	n/a
26	JUND	chr3:195648159-195649101	SK-N-SH	brain:	n/a	chr3:195648373-195648385 chr3:195648374-195648384 chr3:195648375-195648382 chr3:195648373-195648384 chr3:195648374-195648383 chr3:195648375-195648384 chr3:195648375-195648383
27	POLR2A	chr3:195648032-195648725	ECC-1	luminal epithelium:	n/a	n/a
28	MAFK	chr3:195648182-195648606	HepG2	liver:	n/a	chr3:195648376-195648385 chr3:195648266-195648277 chr3:195648369-195648389 chr3:195648373-195648382 chr3:195648375-195648385 chr3:195648378-195648389 chr3:195648374-195648389 chr3:195648371-195648387 chr3:195648372-195648386
29	FOSL2	chr3:195648026-195648675	MCF-7	breast:	n/a	chr3:195648373-195648385 chr3:195648374-195648384 chr3:195648375-195648382 chr3:195648374-195648383 chr3:195648375-195648384 chr3:195648375-195648383
30	NFIC	chr3:195647970-195648865	ECC-1	luminal epithelium:	n/a	n/a
31	MAX	chr3:195647989-195648759	ECC-1	luminal epithelium:	n/a	chr3:195648374-195648383 chr3:195648375-195648384
32	MAFK	chr3:195648105-195648676	K562	blood:	n/a	chr3:195648376-195648385 chr3:195648266-195648277 chr3:195648369-195648389 chr3:195648373-195648382 chr3:195648375-195648385 chr3:195648378-195648389 chr3:195648374-195648389 chr3:195648371-195648387 chr3:195648372-195648386
33	BACH1	chr3:195648206-195648563	H1-hESC	embryonic stem cell:	n/a	chr3:195648372-195648386

No.	Distal block	Cell Line	Cell type
1	chr3:195648186..195651033-chr3:195656557..195658733,2	MCF-7	breast:
2	chr3:195648030..195651795-chr3:195655023..195658077,4	K562	blood:
3	chr3:195640626..195643616-chr3:195648215..195651575,3	MCF-7	breast:
4	chr3:195634752..195636782-chr3:195648139..195650120,2	MCF-7	breast:

Variant related genes	Relation type
RN7SL773P	TF binding region
ENSG00000239122	Chromatin interaction
ENSG00000061938	Chromatin interaction
ENSG00000224614	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs1811139	1.00[CHD][hapmap]
rs842223	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759213	chr3:195102787-196071593	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv1001387	chr3:195186128-195661538	Bivalent Enhancer Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
3	nsv428102	chr3:195201080-195829426	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv428430	chr3:195201080-195829426	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
5	esv2757913	chr3:195379484-196071593	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
6	nsv1006165	chr3:195383130-195777211	Bivalent Enhancer Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
7	nsv471621	chr3:195417664-195795474	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	esv2751988	chr3:195433543-195651349	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
9	esv2756651	chr3:195433543-195696720	Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
10	nsv432528	chr3:195433543-195696720	Enhancers Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
11	esv2754016	chr3:195433543-195753766	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
12	nsv822410	chr3:195438740-195725565	Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
13	nsv1005193	chr3:195526571-195709662	Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
14	nsv530397	chr3:195565159-195740416	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
15	nsv593056	chr3:195571024-195656731	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
16	nsv1007235	chr3:195582468-195651911	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
17	nsv1002629	chr3:195582468-195769275	Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
18	nsv1014602	chr3:195606770-195661538	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
19	nsv829827	chr3:195608866-195760829	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
20	nsv469518	chr3:195623722-195795474	Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
21	nsv482784	chr3:195623722-195795474	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
22	nsv1011404	chr3:195627654-195656614	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
23	nsv1010395	chr3:195641908-195848264	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
24	nsv532213	chr3:195643944-196063636	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
25	nsv967107	chr3:195648362-195697515	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2046969	PPP1R2	cis	cerebellum	SCAN
rs2046969	PRL	trans	cerebellum	SCAN
rs2046969	MUC20	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195642000-195656600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:195642200-195650800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:195645600-195658800	Weak transcription	Fetal Intestine Small	intestine
4	chr3:195647200-195681200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr3:195647800-195648600	Enhancers	Pancreas	Pancrea
6	chr3:195647800-195648800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:195647800-195648800	Enhancers	Esophagus	oesophagus
8	chr3:195648000-195648600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:195648000-195648600	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr3:195648000-195648600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:195648000-195648600	Enhancers	Spleen	Spleen
12	chr3:195648000-195648600	Bivalent Enhancer	HUVEC	blood vessel
13	chr3:195648000-195648600	Flanking Active TSS	NHEK	skin
14	chr3:195648000-195648800	Enhancers	H1 Cell Line	embryonic stem cell
15	chr3:195648000-195648800	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr3:195648000-195648800	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr3:195648000-195648800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:195648000-195648800	Bivalent Enhancer	Placenta	Placenta
19	chr3:195648000-195649000	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr3:195648200-195648600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:195648200-195648600	Enhancers	H9 Cell Line	embryonic stem cell
22	chr3:195648200-195648600	Enhancers	Lung	lung
23	chr3:195648200-195648600	Flanking Active TSS	K562	blood
24	chr3:195648200-195648600	Enhancers	NHDF-Ad	bronchial
25	chr3:195648200-195648800	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr3:195648200-195648800	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr3:195648200-195648800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr3:195648200-195648800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:195648400-195648600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:195648400-195648600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:195648400-195648800	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr3:195648400-195648800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
33	chr3:195648400-195648800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr3:195648400-195648800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr3:195648400-195648800	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr3:195648400-195650800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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