Variant report

Variant	rs1709004
Chromosome Location	chr4:2814148-2814149
allele	A/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	FOXP2	chr4:2813603-2814171	PFSK-1	brain:	n/a	n/a
2	ETS1	chr4:2813661-2814154	GM12878	blood:	n/a	chr4:2813930-2813944 chr4:2813823-2813837 chr4:2813972-2813986 chr4:2813931-2813942 chr4:2813972-2813981
3	POLR2A	chr4:2813774-2814321	GM10847	blood:	n/a	n/a
4	MAX	chr4:2813484-2814755	ECC-1	luminal epithelium:	n/a	chr4:2814485-2814495 chr4:2814277-2814286
5	FOXM1	chr4:2813584-2814156	GM12878	blood:	n/a	n/a
6	RELA	chr4:2813692-2814183	GM19099	blood:	n/a	n/a
7	SP1	chr4:2813582-2814168	GM12878	blood:	n/a	n/a
8	TAF1	chr4:2813529-2814271	PFSK-1	brain:	n/a	n/a
9	GABPA	chr4:2813650-2814221	K562	blood:	n/a	n/a
10	ELF1	chr4:2813527-2814342	GM12878	blood:	n/a	chr4:2813926-2813939 chr4:2814001-2814013 chr4:2813969-2813980
11	POLR2A	chr4:2813598-2814545	GM18526	blood:	n/a	n/a
12	NFIC	chr4:2813408-2814342	ECC-1	luminal epithelium:	n/a	n/a
13	YY1	chr4:2813718-2814160	GM12892	blood:	n/a	chr4:2813881-2813892
14	POLR2A	chr4:2813394-2815108	GM12892	blood:	n/a	n/a
15	RELA	chr4:2813503-2814269	GM18951	blood:	n/a	n/a
16	GABPA	chr4:2813581-2814159	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr4:2813652-2814334	SK-N-MC	brain:	n/a	n/a
18	ZNF263	chr4:2813465-2815744	HEK293-T-REx	kidney:	n/a	chr4:2813988-2813997
19	POLR2A	chr4:2813580-2814231	NB4	blood:	n/a	n/a
20	POLR2A	chr4:2813372-2814453	PFSK-1	brain:	n/a	n/a
21	GABPA	chr4:2813708-2814227	MCF-7	breast:	n/a	n/a
22	SIN3A	chr4:2813863-2814166	GM12878	blood:	n/a	chr4:2813950-2813963
23	POLR2A	chr4:2813626-2814193	ProgFib	skin:	n/a	n/a
24	RUNX3	chr4:2813383-2814467	GM12878	blood:	n/a	n/a
25	POLR2A	chr4:2813485-2814285	GM12892	blood:	n/a	n/a
26	GABPA	chr4:2813555-2814305	HL-60	blood:	n/a	n/a
27	MXI1	chr4:2813568-2814375	GM12878	blood:	n/a	chr4:2814278-2814287
28	PAX5	chr4:2813643-2814315	GM12892	blood:	n/a	chr4:2813930-2813939
29	POLR2A	chr4:2813553-2814181	HCT-116	colon:	n/a	n/a
30	MTA3	chr4:2813221-2816423	GM12878	blood:	n/a	n/a
31	POLR2A	chr4:2813291-2814441	ECC-1	luminal epithelium:	n/a	n/a
32	TCF12	chr4:2813379-2814364	ECC-1	luminal epithelium:	n/a	chr4:2813598-2813608
33	TCF12	chr4:2813840-2814210	GM12878	blood:	n/a	n/a
34	GABPA	chr4:2813333-2814311	HL-60	blood:	n/a	n/a
35	POLR2A	chr4:2813543-2814404	Raji	blood:	n/a	n/a
36	MAX	chr4:2813359-2814594	ECC-1	luminal epithelium:	n/a	chr4:2814485-2814495 chr4:2814277-2814286
37	POLR2A	chr4:2813883-2814194	GM12878	blood:	n/a	n/a
38	PAX5	chr4:2813460-2814384	GM12878	blood:	n/a	chr4:2814325-2814334 chr4:2813930-2813939
39	EP300	chr4:2813798-2814202	GM12878	blood:	n/a	chr4:2813971-2813980 chr4:2814010-2814026
40	YY1	chr4:2813614-2814233	ECC-1	luminal epithelium:	n/a	chr4:2813881-2813892
41	SPI1	chr4:2813710-2814165	GM12891	blood:	n/a	chr4:2813971-2813980
42	POLR2A	chr4:2813513-2814427	GM12878	blood:	n/a	n/a
43	PAX5	chr4:2813828-2814234	GM12878	blood:	n/a	chr4:2813930-2813939
44	BCLAF1	chr4:2813635-2814292	GM12878	blood:	n/a	chr4:2813930-2813939
45	TAF1	chr4:2813652-2814304	ECC-1	luminal epithelium:	n/a	n/a
46	MAX	chr4:2813575-2814400	GM12878	blood:	n/a	chr4:2814277-2814286
47	SIN3AK20	chr4:2813696-2814203	PFSK-1	brain:	n/a	n/a
48	POLR2A	chr4:2813531-2815296	GM18951	blood:	n/a	n/a
49	POLR2A	chr4:2813327-2814450	HL-60	blood:	n/a	n/a
50	POLR2A	chr4:2813221-2814866	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:2814122-2814172	H1-hESC	embryonic stem cell:	embryo
2	chr4:2814122-2814172	HCM	heart:	n/a
3	chr4:2814122-2814172	AG09309	skin:	n/a
4	chr4:2814122-2814172	HCF	heart:	n/a
5	chr4:2814122-2814172	HAEpiC	amniotic membrane:	n/a
6	chr4:2814122-2814172	HRCEpiC	kidney:	n/a
7	chr4:2814122-2814172	MCF-7	breast:	n/a
8	chr4:2814122-2814172	NHBE	bronchial:	n/a
9	chr4:2814122-2814172	A549	lung:	n/a
10	chr4:2814122-2814172	SK-N-SH_RA	brain:	n/a
11	chr4:2814122-2814172	HPAEpiC	pulmonary alveolar:	n/a
12	chr4:2814122-2814172	IMR90	lung:	fetal
13	chr4:2814122-2814172	GM06990	blood:	n/a
14	chr4:2814122-2814172	HIPEpiC	eye:	n/a
15	chr4:2814122-2814172	GM12891	blood:	n/a
16	chr4:2814122-2814172	HEK293	kidney:	embryo
17	chr4:2814122-2814172	HCPEpiC	choroid plexus:	n/a
18	chr4:2814122-2814172	PrEC	prostate:	n/a
19	chr4:2814122-2814172	SK-N-SH	brain:	n/a
20	chr4:2814122-2814172	Hepatocyte	liver:	n/a
21	chr4:2814122-2814172	HMEC	breast:	n/a
22	chr4:2814122-2814172	Caco-2	colon:	n/a
23	chr4:2814122-2814172	Hela-S3	cervix:	n/a
24	chr4:2814122-2814172	AG04449	skin:	fetal
25	chr4:2814122-2814172	NHDF-neo	bronchial:	n/a
26	chr4:2814122-2814172	AoSMC	blood vessel:	n/a
27	chr4:2814122-2814172	BJ	skin:	n/a
28	chr4:2814122-2814172	GM12878	blood:	n/a
29	chr4:2814122-2814172	HRPEpiC	eye:	n/a
30	chr4:2814122-2814172	HNPCEpiC	eye:	n/a
31	chr4:2814122-2814172	HUVEC	blood vessel:	n/a
32	chr4:2814122-2814172	RPTEC	kidney:	n/a
33	chr4:2814122-2814172	HL-60	blood:	n/a
34	chr4:2814122-2814172	HCT-116	colon:	n/a
35	chr4:2814122-2814172	PFSK-1	brain:	n/a
36	chr4:2814122-2814172	SK-N-MC	brain:	n/a
37	chr4:2814122-2814172	NT2-D1	testis:	n/a
38	chr4:2814122-2814172	AG09319	gingival:	n/a
39	chr4:2814122-2814172	K562	blood:	n/a
40	chr4:2814122-2814172	HEEpiC	esophagus:	n/a
41	chr4:2814122-2814172	LNCaP	prostate:	n/a
42	chr4:2814122-2814172	SKMC	muscle:	n/a
43	chr4:2814122-2814172	CMK	blood:	n/a
44	chr4:2814122-2814172	PANC-1	pancreas:	n/a
45	chr4:2814122-2814172	AG10803	skin:	n/a
46	chr4:2814122-2814172	Jurkat	blood:	n/a
47	chr4:2814122-2814172	GM19239	blood:	n/a
48	chr4:2814122-2814172	BE2_C	brain:	n/a
49	chr4:2814122-2814172	GM12892	blood:	n/a
50	chr4:2814122-2814172	ECC-1	luminal epithelium:	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:2812096..2814174-chr4:2819979..2821555,2	MCF-7	breast:
2	chr4:2812607..2814330-chr4:2927336..2930211,2	MCF-7	breast:
3	chr4:2811128..2813446-chr4:2813847..2818794,5	MCF-7	breast:

Variant related genes	Relation type
SH3BP2	TF binding region
SH3BP2	CpG island
ENSG00000087274	Chromatin interaction
ENSG00000087266	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs231706	1.00[CEU][hapmap]
rs55977536	0.88[EUR][1000 genomes]
rs73794806	0.88[EUR][1000 genomes]
rs7677070	1.00[CEU][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948659	chr4:1828867-2815632	ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	nsv878444	chr4:2689449-2861090	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv470002	chr4:2701098-2836628	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv878445	chr4:2704046-2831383	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv878447	chr4:2723531-2831383	Flanking Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Enhancers Strong transcription Active 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 target site	19 gene(s)	inside rSNPs	diseases
6	nsv516797	chr4:2723531-2836628	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv878448	chr4:2723531-2846799	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
9	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
10	nsv878449	chr4:2744480-2831383	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv1002517	chr4:2747905-2822017	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
12	nsv878450	chr4:2760222-2861090	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
13	nsv593435	chr4:2770772-2881256	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	nsv878451	chr4:2785556-2856687	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	nsv878452	chr4:2789184-2830076	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv1010533	chr4:2792848-2873441	Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
17	nsv461162	chr4:2794320-2846799	Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
18	nsv593436	chr4:2794320-2846799	Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2796600-2814600	Enhancers	Stomach Mucosa	stomach
2	chr4:2803400-2819200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr4:2806000-2814600	Enhancers	Liver	Liver
4	chr4:2809200-2815200	Weak transcription	Fetal Brain Female	brain
5	chr4:2811000-2815200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:2811000-2816000	Enhancers	Brain Substantia Nigra	brain
7	chr4:2811200-2814200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr4:2811200-2814600	Enhancers	Brain Anterior Caudate	brain
9	chr4:2811200-2814600	Genic enhancers	Fetal Intestine Small	intestine
10	chr4:2811200-2815000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr4:2811400-2814800	Enhancers	H1 Cell Line	embryonic stem cell
12	chr4:2811600-2815400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:2811800-2814400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:2811800-2815200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr4:2811800-2819400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr4:2812000-2815400	Weak transcription	Fetal Heart	heart
17	chr4:2812200-2815200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr4:2812400-2815200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr4:2812600-2815200	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr4:2812600-2815600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr4:2812800-2815200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr4:2813000-2814600	Enhancers	NHDF-Ad	bronchial
23	chr4:2813000-2815200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr4:2813200-2814200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:2813200-2815200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr4:2813200-2815400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr4:2813200-2815400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr4:2813200-2815600	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr4:2813200-2815600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr4:2813200-2815600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr4:2813200-2816000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr4:2813400-2814200	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr4:2813400-2814200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr4:2813400-2814200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr4:2813400-2814200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr4:2813400-2814200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr4:2813400-2814200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
38	chr4:2813400-2814200	Flanking Active TSS	Colonic Mucosa	Colon
39	chr4:2813400-2814200	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr4:2813400-2814200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
41	chr4:2813400-2814200	Flanking Active TSS	GM12878-XiMat	blood
42	chr4:2813400-2814400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
43	chr4:2813400-2814800	Enhancers	Fetal Lung	lung
44	chr4:2813400-2815000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
45	chr4:2813400-2815000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
46	chr4:2813400-2815200	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr4:2813400-2815400	Flanking Active TSS	Primary B cells from cord blood	blood
48	chr4:2813400-2815400	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr4:2813400-2815400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr4:2813400-2815400	Active TSS	Rectal Smooth Muscle	rectum

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