Variant report

Variant	rs12878084
Chromosome Location	chr14:21945629-21945630
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:189)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:189 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:21944565-21945671	HepG2	liver:	n/a	n/a
2	YY1	chr14:21944614-21945932	HepG2	liver:	n/a	chr14:21945140-21945151 chr14:21945135-21945146 chr14:21944915-21944924 chr14:21944912-21944921
3	HEY1	chr14:21945166-21945894	K562	blood:	n/a	n/a
4	BHLHE40	chr14:21944452-21945654	HepG2	liver:	n/a	n/a
5	RUNX3	chr14:21944555-21945735	GM12878	blood:	n/a	n/a
6	MTA3	chr14:21944537-21945764	GM12878	blood:	n/a	n/a
7	MXI1	chr14:21943930-21946175	SK-N-SH	brain:	n/a	n/a
8	MAX	chr14:21945047-21945651	ECC-1	luminal epithelium:	n/a	n/a
9	TAF1	chr14:21944576-21945882	HepG2	liver:	n/a	n/a
10	GABPA	chr14:21944890-21945781	SK-N-SH	brain:	n/a	chr14:21944912-21944921
11	HCFC1	chr14:21944639-21945651	K562	blood:	n/a	n/a
12	POLR2A	chr14:21944543-21945916	K562	blood:	n/a	n/a
13	POLR2A	chr14:21944625-21945637	Gliobla	brain:	n/a	n/a
14	POLR2A	chr14:21944677-21945780	GM12892	blood:	n/a	n/a
15	CEBPD	chr14:21944588-21945641	HepG2	liver:	n/a	n/a
16	POLR2A	chr14:21945105-21945694	K562	blood:	n/a	n/a
17	POLR2A	chr14:21945175-21945631	HepG2	liver:	n/a	n/a
18	MAX	chr14:21944996-21945713	NB4	blood:	n/a	n/a
19	MXI1	chr14:21944519-21945655	Hela-S3	cervix:	n/a	n/a
20	GABPA	chr14:21944471-21945884	MCF-7	breast:	n/a	chr14:21944912-21944921
21	POLR2A	chr14:21944630-21945731	GM19193	blood:	n/a	n/a
22	SIN3AK20	chr14:21944379-21945978	MCF-7	breast:	n/a	n/a
23	MAZ	chr14:21944485-21945757	GM12878	blood:	n/a	chr14:21944916-21944926
24	HEY1	chr14:21945245-21945632	K562	blood:	n/a	n/a
25	NFYB	chr14:21944932-21945640	GM12878	blood:	n/a	n/a
26	POLR2A	chr14:21944624-21945742	HL-60	blood:	n/a	n/a
27	ZNF143	chr14:21944633-21945641	GM12878	blood:	n/a	n/a
28	ELK1	chr14:21945205-21945739	K562	blood:	n/a	n/a
29	GABPA	chr14:21945026-21945683	A549	lung:	n/a	n/a
30	GABPA	chr14:21944914-21945807	HL-60	blood:	n/a	n/a
31	TAF1	chr14:21944534-21945633	ECC-1	luminal epithelium:	n/a	n/a
32	CREB1	chr14:21944779-21945828	GM12878	blood:	n/a	n/a
33	GABPA	chr14:21944964-21945639	HL-60	blood:	n/a	n/a
34	POLR2A	chr14:21944602-21945660	ECC-1	luminal epithelium:	n/a	n/a
35	ELK4	chr14:21945210-21945722	Hela-S3	cervix:	n/a	chr14:21945355-21945366
36	POLR2A	chr14:21944603-21945757	A549	lung:	n/a	n/a
37	POLR2A	chr14:21944359-21945843	Hela-S3	cervix:	n/a	n/a
38	PML	chr14:21945148-21945676	MCF-7	breast:	n/a	n/a
39	POLR2A	chr14:21945164-21945634	H1-hESC	embryonic stem cell:	n/a	n/a
40	MAX	chr14:21944536-21945652	SK-N-SH	brain:	n/a	chr14:21944916-21944926
41	POLR2A	chr14:21944891-21945700	GM12891	blood:	n/a	n/a
42	POLR2A	chr14:21944609-21945966	H1-neurons	neurons:	n/a	n/a
43	CHD2	chr14:21944636-21945790	HepG2	liver:	n/a	n/a
44	POLR2A	chr14:21944244-21945802	HepG2	liver:	n/a	n/a
45	YY1	chr14:21944839-21945629	GM12878	blood:	n/a	chr14:21945140-21945151 chr14:21945135-21945146 chr14:21944915-21944924 chr14:21944912-21944921
46	REST	chr14:21944432-21946042	H1-neurons	neurons:	n/a	n/a
47	GABPA	chr14:21944569-21945791	SK-N-SH	brain:	n/a	chr14:21944912-21944921
48	CHD1	chr14:21945095-21945654	GM12878	blood:	n/a	n/a
49	POLR2A	chr14:21944596-21945908	H1-neurons	neurons:	n/a	n/a
50	FOXM1	chr14:21945025-21945764	MCF-7	breast:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:21944743..21947528-chr14:21994092..21996767,2	MCF-7	breast:
2	chr14:21923260..21925455-chr14:21943748..21947334,4	K562	blood:
3	chr14:21943182..21946742-chr14:21976824..21981257,10	MCF-7	breast:
4	chr14:21903784..21905572-chr14:21943555..21945925,2	MCF-7	breast:
5	chr14:21922721..21925394-chr14:21943917..21947287,10	MCF-7	breast:
6	chr1:149858313..149859863-chr14:21943720..21946355,2	MCF-7	breast:
7	chr14:21903666..21907303-chr14:21944223..21946943,4	K562	blood:
8	chr14:21922608..21930261-chr14:21941288..21947915,21	MCF-7	breast:
9	chr14:21943174..21947446-chr14:21976603..21980796,8	K562	blood:
10	chr14:21943699..21946735-chr14:21977733..21982256,4	MCF-7	breast:
11	chr14:21944239..21947571-chr14:21970430..21973821,4	MCF-7	breast:
12	chr14:21941797..21947093-chr14:21954513..21961521,11	MCF-7	breast:

No data

Variant related genes	Relation type
RAB2B	TF binding region
ENSG00000178096	Chromatin interaction
ENSG00000100888	Chromatin interaction
ENSG00000165821	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000165819	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000092203	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1045811	1.00[CHD][hapmap];0.85[MEX][hapmap]
rs1045812	1.00[CHD][hapmap];0.90[MEX][hapmap]
rs10483252	0.81[MEX][hapmap]
rs1061026	1.00[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12880071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12884313	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12891263	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12894578	1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17106448	1.00[CHD][hapmap];0.85[MEX][hapmap]
rs17106830	1.00[CEU][hapmap];0.93[GIH][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs33919729	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34765612	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35446048	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35463722	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35582631	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35856604	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3752411	1.00[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3762161	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4981372	0.88[CHD][hapmap];0.90[MEX][hapmap]
rs4982449	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4982451	1.00[CEU][hapmap]
rs56144428	0.81[AMR][1000 genomes]
rs67492181	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67802283	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73581403	0.88[AMR][1000 genomes]
rs73581411	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73581416	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73581419	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9322989	0.93[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530009	chr14:21377022-22044608	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
2	nsv530769	chr14:21407536-22139126	Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
3	nsv1036762	chr14:21507093-22101805	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	nsv541976	chr14:21507093-22101805	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
5	esv3518898	chr14:21805983-22077584	Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	esv3518899	chr14:21805983-22077584	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv1054013	chr14:21868964-21992109	Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv541991	chr14:21868964-21992109	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv530011	chr14:21876973-21985341	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	esv2422459	chr14:21931624-22169502	Genic enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer 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	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12878084	ANG	cis	parietal	SCAN
rs12878084	RNF31	cis	parietal	SCAN
rs12878084	METTL3	cis	lymphoblastoid	seeQTL
rs12878084	LTB4R	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:21943800-21946000	Active TSS	Brain Anterior Caudate	brain
2	chr14:21943800-21946000	Active TSS	Rectal Smooth Muscle	rectum
3	chr14:21943800-21946400	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr14:21943800-21946400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr14:21943800-21946600	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr14:21943800-21946800	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr14:21943800-21946800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr14:21943800-21946800	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr14:21944000-21945800	Active TSS	Colonic Mucosa	Colon
10	chr14:21944000-21946000	Active TSS	Esophagus	oesophagus
11	chr14:21944000-21946000	Active TSS	Fetal Brain Male	brain
12	chr14:21944000-21946200	Active TSS	Lung	lung
13	chr14:21944000-21946200	Active TSS	Right Atrium	heart
14	chr14:21944000-21946400	Active TSS	K562	blood
15	chr14:21944000-21946800	Active TSS	H1 Cell Line	embryonic stem cell
16	chr14:21944200-21946000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr14:21944200-21946000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr14:21944200-21946000	Active TSS	Placenta	Placenta
19	chr14:21944200-21946000	Active TSS	Placenta Amnion	Placenta Amnion
20	chr14:21944200-21946000	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr14:21944200-21946000	Active TSS	Stomach Smooth Muscle	stomach
22	chr14:21944200-21946200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr14:21944200-21946200	Active TSS	Muscle Satellite Cultured Cells	--
24	chr14:21944200-21946200	Active TSS	Fetal Intestine Large	intestine
25	chr14:21944200-21946200	Active TSS	Pancreas	Pancrea
26	chr14:21944200-21946200	Active TSS	Thymus	Thymus
27	chr14:21944200-21946200	Bivalent/Poised TSS	HepG2	liver
28	chr14:21944200-21946400	Active TSS	H9 Cell Line	embryonic stem cell
29	chr14:21944200-21946400	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr14:21944200-21946400	Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr14:21944200-21946400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr14:21944200-21946400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr14:21944200-21946400	Active TSS	Fetal Thymus	thymus
34	chr14:21944200-21946400	Active TSS	A549	lung
35	chr14:21944200-21946600	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr14:21944200-21946600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr14:21944200-21946600	Active TSS	Fetal Intestine Small	intestine
38	chr14:21944200-21946600	Active TSS	Fetal Kidney	kidney
39	chr14:21944200-21946800	Active TSS	HMEC	breast
40	chr14:21944200-21946800	Active TSS	NHDF-Ad	bronchial
41	chr14:21944200-21946800	Active TSS	NHLF	lung
42	chr14:21944200-21947000	Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr14:21944400-21945800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr14:21944400-21945800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
45	chr14:21944400-21945800	Active TSS	Liver	Liver
46	chr14:21944400-21945800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
47	chr14:21944400-21946000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr14:21944400-21946000	Active TSS	Brain Cingulate Gyrus	brain
49	chr14:21944400-21946000	Active TSS	Brain Substantia Nigra	brain
50	chr14:21944400-21946000	Active TSS	Colon Smooth Muscle	Colon

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