Variant report

Variant	rs4764430
Chromosome Location	chr12:10517808-10517809
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:140)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:140 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD2	chr12:10517443-10518113	H1-hESC	embryonic stem cell:	n/a	n/a
2	RELA	chr12:10516765-10517988	GM19099	blood:	n/a	n/a
3	RUNX3	chr12:10515233-10518021	GM12878	blood:	n/a	n/a
4	SP1	chr12:10517455-10518254	H1-hESC	embryonic stem cell:	n/a	n/a
5	STAT3	chr12:10517612-10518076	Hela-S3	cervix:	n/a	n/a
6	ATF2	chr12:10517788-10518192	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr12:10516544-10517857	GM12878	blood:	n/a	n/a
8	MAX	chr12:10517676-10517946	H1-hESC	embryonic stem cell:	n/a	n/a
9	RAD21	chr12:10517469-10518122	ECC-1	luminal epithelium:	n/a	n/a
10	MAFK	chr12:10517487-10518231	IMR90	lung:	n/a	n/a
11	POLR2A	chr12:10516250-10517851	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr12:10516468-10517960	Hela-S3	cervix:	n/a	n/a
13	JUND	chr12:10517691-10518041	H1-hESC	embryonic stem cell:	n/a	n/a
14	ELK1	chr12:10517034-10518070	Hela-S3	cervix:	n/a	n/a
15	STAT1	chr12:10516853-10517993	GM12878	blood:	n/a	n/a
16	USF2	chr12:10517132-10518059	Hela-S3	cervix:	n/a	n/a
17	CEBPB	chr12:10517435-10518128	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr12:10516740-10518137	HCT-116	colon:	n/a	n/a
19	POLR2A	chr12:10516072-10518073	GM12891	blood:	n/a	n/a
20	CHD2	chr12:10517449-10518385	Hela-S3	cervix:	n/a	n/a
21	IRF4	chr12:10516507-10517862	GM12878	blood:	n/a	chr12:10517695-10517716
22	JUN	chr12:10517618-10517971	H1-hESC	embryonic stem cell:	n/a	n/a
23	MXI1	chr12:10517154-10517997	H1-hESC	embryonic stem cell:	n/a	n/a
24	TBL1XR1	chr12:10516939-10518035	GM12878	blood:	n/a	n/a
25	MAX	chr12:10517158-10518411	Hela-S3	cervix:	n/a	n/a
26	ZNF143	chr12:10517458-10518184	K562	blood:	n/a	n/a
27	POLR2A	chr12:10516552-10517869	K562	blood:	n/a	n/a
28	SIN3AK20	chr12:10517545-10517809	H1-hESC	embryonic stem cell:	n/a	n/a
29	USF1	chr12:10517539-10518029	ECC-1	luminal epithelium:	n/a	n/a
30	STAT3	chr12:10516851-10518033	GM12878	blood:	n/a	n/a
31	NFATC1	chr12:10516719-10517917	GM12878	blood:	n/a	n/a
32	POLR2A	chr12:10517355-10517829	U87	brain:	n/a	n/a
33	HCFC1	chr12:10517515-10517833	K562	blood:	n/a	n/a
34	TCF7L2	chr12:10517374-10518553	PANC-1	pancreas:	n/a	n/a
35	IRF1	chr12:10515959-10518392	K562	blood:	n/a	chr12:10517695-10517716
36	POLR2A	chr12:10517325-10517945	U87	brain:	n/a	n/a
37	RAD21	chr12:10517561-10518135	Hela-S3	cervix:	n/a	n/a
38	RCOR1	chr12:10516690-10517857	GM12878	blood:	n/a	n/a
39	MAX	chr12:10516789-10518108	A549	lung:	n/a	n/a
40	FOXM1	chr12:10516639-10517966	GM12878	blood:	n/a	n/a
41	SP1	chr12:10517485-10518158	H1-hESC	embryonic stem cell:	n/a	n/a
42	SMC3	chr12:10517690-10517976	GM12878	blood:	n/a	n/a
43	MAFK	chr12:10517777-10518253	H1-hESC	embryonic stem cell:	n/a	n/a
44	NFIC	chr12:10515243-10518076	GM12878	blood:	n/a	n/a
45	BRCA1	chr12:10517548-10518007	Hela-S3	cervix:	n/a	n/a
46	TCF7L2	chr12:10516387-10518166	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr12:10516590-10518268	SK-N-MC	brain:	n/a	n/a
48	TCF7L2	chr12:10517720-10518393	HEK293	kidney:	n/a	n/a
49	FOXM1	chr12:10515269-10517964	GM12878	blood:	n/a	n/a
50	RCOR1	chr12:10517670-10518084	K562	blood:	n/a	n/a

No data

Variant related genes	Relation type
ENSG00000256155	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1049172	0.81[CHD][hapmap]
rs10743887	0.82[ASN][1000 genomes]
rs10743888	0.86[EUR][1000 genomes]
rs10743889	0.85[EUR][1000 genomes]
rs10772267	0.82[JPT][hapmap]
rs1351113	0.81[CHD][hapmap]
rs1382264	0.93[CEU][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs1382265	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs1478309	0.93[CEU][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs1478310	0.87[EUR][1000 genomes]
rs1600127	0.89[EUR][1000 genomes]
rs2045876	0.87[EUR][1000 genomes]
rs2100923	0.85[EUR][1000 genomes]
rs2126888	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2126889	0.89[EUR][1000 genomes]
rs2246809	0.93[CEU][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs2255336	0.93[CEU][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs2255353	0.89[EUR][1000 genomes]
rs2255364	0.87[CEU][hapmap];0.89[EUR][1000 genomes]
rs2417734	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs2617151	0.93[CEU][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs2617152	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs2617156	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs2617157	0.89[EUR][1000 genomes]
rs2617169	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2617172	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2733840	0.93[CEU][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2733845	0.93[CEU][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs2733847	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs2733848	0.83[EUR][1000 genomes]
rs2733853	0.83[EUR][1000 genomes]
rs2734414	0.87[CEU][hapmap];0.80[TSI][hapmap]
rs2734561	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs2927561	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs4415856	1.00[JPT][hapmap]
rs6488285	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7139147	0.82[ASN][1000 genomes]
rs7301582	1.00[JPT][hapmap]
rs7307721	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7310643	0.86[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7397310	0.86[EUR][1000 genomes]
rs7956385	0.82[ASN][1000 genomes]
rs7957681	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7958658	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7959328	0.82[ASN][1000 genomes]
rs7964772	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7965744	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7980379	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898757	chr12:10229281-10614641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv832328	chr12:10398071-10620443	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv898759	chr12:10454556-10583365	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv3432683	chr12:10470734-10527581	Genic enhancers Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	esv3351751	chr12:10472734-10522269	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv898760	chr12:10492982-10564329	Genic enhancers Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv898761	chr12:10496724-10564329	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv1036390	chr12:10496724-10596720	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv557455	chr12:10508975-10560957	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription 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	9 gene(s)	inside rSNPs	diseases
10	nsv898762	chr12:10509383-10564329	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
11	nsv898763	chr12:10514528-10603670	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer 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 target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs4764430	C12orf53	cis	cerebellum	SCAN
rs4764430	KLRC3	cis	parietal	SCAN
rs4764430	KLRC2	cis	cerebellum	SCAN
rs4764430	ZNF384	cis	cerebellum	SCAN
rs4764430	KLRC4	cis	lesional skin	skin_eQTL
rs4764430	LRRC23	cis	cerebellum	SCAN
rs4764430	KLRC4	cis	cerebellum	SCAN
rs4764430	GNB3	cis	cerebellum	SCAN
rs4764430	KLRK1	cis	lymphoblastoid	seeQTL
rs4764430	KLRC2	cis	parietal	SCAN
rs4764430	C1S	cis	cerebellum	SCAN
rs4764430	KLRK1	cis	parietal	SCAN
rs4764430	KLRC4	cis	parietal	SCAN
rs4764430	CHD4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10515200-10518600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
2	chr12:10515400-10518600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr12:10515600-10518200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:10515600-10518200	Active TSS	Brain Anterior Caudate	brain
5	chr12:10515800-10518200	Active TSS	Fetal Kidney	kidney
6	chr12:10516000-10518000	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr12:10516000-10518200	Active TSS	Colon Smooth Muscle	Colon
8	chr12:10516000-10518200	Active TSS	Fetal Stomach	stomach
9	chr12:10516000-10518400	Active TSS	K562	blood
10	chr12:10516200-10518400	Active TSS	Ovary	ovary
11	chr12:10516200-10518800	Flanking Active TSS	HUVEC	blood vessel
12	chr12:10516400-10518000	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr12:10516400-10518000	Active TSS	Gastric	stomach
14	chr12:10516400-10518000	Active TSS	Sigmoid Colon	Sigmoid Colon
15	chr12:10516400-10518000	Active TSS	Spleen	Spleen
16	chr12:10516400-10518200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr12:10516400-10518200	Active TSS	Esophagus	oesophagus
18	chr12:10516400-10518200	Active TSS	Psoas Muscle	Psoas
19	chr12:10516400-10518200	Active TSS	Right Ventricle	heart
20	chr12:10516400-10518600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr12:10516400-10518600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:10516400-10519200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:10516600-10518000	Active TSS	Thymus	Thymus
24	chr12:10516600-10518000	Bivalent/Poised TSS	HepG2	liver
25	chr12:10516600-10518200	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr12:10516600-10518200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr12:10516600-10518200	Active TSS	Brain Hippocampus Middle	brain
28	chr12:10516600-10518200	Active TSS	Fetal Intestine Large	intestine
29	chr12:10516600-10518200	Active TSS	Left Ventricle	heart
30	chr12:10516600-10518200	Active TSS	Right Atrium	heart
31	chr12:10516600-10518200	Active TSS	NHDF-Ad	bronchial
32	chr12:10516600-10518600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
33	chr12:10516600-10518800	Flanking Active TSS	Primary B cells from cord blood	blood
34	chr12:10516600-10518800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr12:10516800-10518000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
36	chr12:10516800-10518000	Active TSS	Stomach Mucosa	stomach
37	chr12:10516800-10518200	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr12:10516800-10518200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr12:10516800-10518200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr12:10516800-10518200	Active TSS	Brain Germinal Matrix	brain
41	chr12:10516800-10518200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr12:10516800-10518400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr12:10516800-10518400	Active TSS	Aorta	Aorta
44	chr12:10516800-10518400	Active TSS	Brain Angular Gyrus	brain
45	chr12:10516800-10518600	Flanking Active TSS	Primary hematopoietic stem cells	blood
46	chr12:10516800-10518600	Active TSS	Fetal Muscle Trunk	muscle
47	chr12:10516800-10518600	Flanking Active TSS	Dnd41	blood
48	chr12:10517000-10518000	Active TSS	Lung	lung
49	chr12:10517000-10518000	Active TSS	Monocytes-CD14+_RO01746	blood
50	chr12:10517000-10518200	Active TSS	iPS-20b Cell Line	embryonic stem cell

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