Variant report

Variant	rs10771309
Chromosome Location	chr12:9218606-9218607
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:9216895-9230988	HepG2	liver:	n/a	n/a
2	MBD4	chr12:9218319-9219866	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:9216806-9219983	HepG2	liver:	n/a	n/a
4	CHD2	chr12:9217996-9219810	HepG2	liver:	n/a	n/a
5	POLR2A	chr12:9216389-9221070	HepG2	liver:	n/a	n/a
6	MYBL2	chr12:9218472-9220191	HepG2	liver:	n/a	n/a
7	POLR2A	chr12:9217415-9220251	HepG2	liver:	n/a	n/a
8	POLR2A	chr12:9216589-9220417	HepG2	liver:	n/a	n/a
9	MBD4	chr12:9218464-9220244	HepG2	liver:	n/a	n/a
10	JUND	chr12:9218573-9219550	HepG2	liver:	n/a	n/a
11	MYBL2	chr12:9218164-9218777	HepG2	liver:	n/a	n/a
12	NFIC	chr12:9218583-9220189	HepG2	liver:	n/a	n/a
13	MAFK	chr12:9218323-9218614	HepG2	liver:	n/a	n/a
14	POLR2A	chr12:9218510-9218685	MCF10A-Er-Src	breast:	n/a	n/a
15	SETDB1	chr12:9218231-9218813	U2OS	brain:	n/a	n/a
16	NFIC	chr12:9218587-9219470	HepG2	liver:	n/a	n/a
17	POLR2A	chr12:9216161-9220988	HepG2	liver:	n/a	n/a
18	ZNF263	chr12:9216574-9218618	HEK293-T-REx	kidney:	n/a	chr12:9217478-9217487
19	FOSL2	chr12:9217444-9219607	HepG2	liver:	n/a	n/a
20	CREB1	chr12:9216657-9219423	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:9218102..9220634-chr12:9230847..9232385,2	MCF-7	breast:
2	chr12:9064962..9066827-chr12:9216213..9218614,2	MCF-7	breast:
3	chr12:9218454..9221005-chr12:9232709..9234704,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLRG1-1	chr12:9218422-9219303	NONHSAT026384

No data

Variant related genes	Relation type
LINC00612	TF binding region
ENSG00000111752	Chromatin interaction
ENSG00000175899	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10743598	0.93[CHD][hapmap]
rs10771307	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10771310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10842789	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10842795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10842820	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10842845	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10842898	0.96[CEU][hapmap];0.81[CHB][hapmap];0.94[EUR][1000 genomes]
rs11048789	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs113973	0.93[CHD][hapmap]
rs1805651	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1805652	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1805653	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1805654	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1805655	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1805656	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1805657	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1805658	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1805659	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1805660	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1805662	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs1805663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs1805664	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1805666	0.90[CHB][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1805667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1805678	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1805681	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2193005	0.96[CEU][hapmap];0.90[CHB][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs226379	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs226380	0.93[CHD][hapmap]
rs226383	0.94[EUR][1000 genomes]
rs226384	0.91[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs226386	0.93[CHD][hapmap]
rs226388	1.00[CHD][hapmap]
rs226389	0.93[CHD][hapmap]
rs226393	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs226395	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[EUR][1000 genomes]
rs226408	0.93[CHD][hapmap]
rs2300147	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2300148	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2377682	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6487574	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6487581	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6487585	0.81[CHB][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6487587	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs669	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7135781	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7299282	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7299600	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7309361	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7310089	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7310167	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7310884	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7310921	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7955940	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7965184	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7968640	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7976461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs881376	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832327	chr12:9081779-9246220	Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1045317	chr12:9113216-9544655	Weak transcription Enhancers Flanking Active TSS Active TSS 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 miRNA	38 gene(s)	inside rSNPs	diseases
3	nsv898738	chr12:9205030-9274394	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1048491	chr12:9208806-9544655	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10771309	CLECL1	cis	parietal	SCAN
rs10771309	PHC1	cis	multi-tissue	Pritchard

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9216800-9218800	Active TSS	Fetal Lung	lung
2	chr12:9217400-9223400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr12:9217600-9223200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr12:9217800-9218800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
5	chr12:9217800-9218800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr12:9217800-9218800	Flanking Active TSS	Stomach Smooth Muscle	stomach
7	chr12:9217800-9219200	Enhancers	Gastric	stomach
8	chr12:9217800-9220400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr12:9217800-9225000	Weak transcription	Small Intestine	intestine
10	chr12:9217800-9234200	Weak transcription	Primary T cells from cord blood	blood
11	chr12:9218000-9218800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr12:9218000-9218800	Flanking Active TSS	Colon Smooth Muscle	Colon
13	chr12:9218000-9218800	ZNF genes & repeats	Fetal Intestine Small	intestine
14	chr12:9218000-9219000	ZNF genes & repeats	Spleen	Spleen
15	chr12:9218000-9219200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:9218000-9220000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:9218000-9226800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr12:9218000-9234000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr12:9218200-9219000	ZNF genes & repeats	Placenta	Placenta
20	chr12:9218200-9219000	Flanking Active TSS	HepG2	liver
21	chr12:9218200-9219200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr12:9218200-9219200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr12:9218200-9219200	ZNF genes & repeats	Fetal Stomach	stomach
24	chr12:9218200-9219600	Enhancers	Fetal Intestine Large	intestine
25	chr12:9218200-9220000	Enhancers	Hela-S3	cervix
26	chr12:9218200-9220000	Enhancers	HMEC	breast
27	chr12:9218200-9223000	Weak transcription	Aorta	Aorta
28	chr12:9218200-9223200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr12:9218200-9224200	Weak transcription	Ovary	ovary
30	chr12:9218200-9232200	Weak transcription	Fetal Muscle Leg	muscle
31	chr12:9218200-9236200	Weak transcription	Psoas Muscle	Psoas
32	chr12:9218200-9266200	Weak transcription	Fetal Kidney	kidney
33	chr12:9218400-9218800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:9218400-9218800	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr12:9218400-9218800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr12:9218400-9218800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr12:9218400-9218800	Enhancers	Fetal Heart	heart
38	chr12:9218400-9219000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr12:9218400-9219000	Enhancers	Left Ventricle	heart
40	chr12:9218400-9219000	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr12:9218400-9219200	Enhancers	Esophagus	oesophagus
42	chr12:9218400-9219200	Enhancers	Pancreas	Pancrea
43	chr12:9218400-9219800	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr12:9218400-9220000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr12:9218400-9220200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr12:9218400-9220200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr12:9218400-9220400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:9218400-9223800	Weak transcription	Duodenum Mucosa	Duodenum
49	chr12:9218400-9224200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr12:9218400-9224200	Weak transcription	Rectal Mucosa Donor 29	rectum

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