Variant report

Variant	rs10771307
Chromosome Location	chr12:9218201-9218202
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:42)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:42 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr12:9216723-9218224	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr12:9216895-9230988	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:9217762-9218201	HepG2	liver:	n/a	n/a
4	POLR2A	chr12:9216806-9219983	HepG2	liver:	n/a	n/a
5	CHD2	chr12:9217996-9219810	HepG2	liver:	n/a	n/a
6	POLR2A	chr12:9216389-9221070	HepG2	liver:	n/a	n/a
7	POLR2A	chr12:9216782-9218494	HepG2	liver:	n/a	n/a
8	MBD4	chr12:9217946-9218417	HepG2	liver:	n/a	n/a
9	NR2C2	chr12:9217015-9218395	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr12:9217415-9220251	HepG2	liver:	n/a	n/a
11	TCF12	chr12:9216607-9218377	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr12:9216589-9220417	HepG2	liver:	n/a	n/a
13	BACH1	chr12:9216722-9218327	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr12:9216772-9218342	H1-hESC	embryonic stem cell:	n/a	n/a
15	TAF1	chr12:9216803-9218264	HepG2	liver:	n/a	n/a
16	MYBL2	chr12:9218164-9218777	HepG2	liver:	n/a	n/a
17	MAX	chr12:9217200-9218412	HepG2	liver:	n/a	n/a
18	CTBP2	chr12:9216782-9218277	H1-hESC	embryonic stem cell:	n/a	n/a
19	RCOR1	chr12:9216671-9218459	Hela-S3	cervix:	n/a	n/a
20	MAX	chr12:9216737-9218529	HepG2	liver:	n/a	n/a
21	POLR2A	chr12:9216491-9218217	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr12:9216657-9218399	MCF-7	breast:	n/a	n/a
23	JUND	chr12:9217747-9218356	HepG2	liver:	n/a	n/a
24	RFX5	chr12:9217924-9218475	HepG2	liver:	n/a	n/a
25	MXI1	chr12:9216742-9218293	HepG2	liver:	n/a	n/a
26	RCOR1	chr12:9216730-9218324	HepG2	liver:	n/a	n/a
27	POLR2A	chr12:9216230-9218354	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr12:9216734-9218359	A549	lung:	n/a	n/a
29	POLR2A	chr12:9216161-9220988	HepG2	liver:	n/a	n/a
30	CTCF	chr12:9218080-9218230	GM12864	blood:	n/a	n/a
31	ZNF263	chr12:9216574-9218618	HEK293-T-REx	kidney:	n/a	chr12:9217478-9217487
32	MAX	chr12:9216744-9218351	ECC-1	luminal epithelium:	n/a	n/a
33	TAF1	chr12:9216663-9218213	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr12:9216528-9218226	MCF-7	breast:	n/a	n/a
35	FOSL2	chr12:9217444-9219607	HepG2	liver:	n/a	n/a
36	POLR2A	chr12:9216722-9218369	MCF-7	breast:	n/a	n/a
37	YY1	chr12:9216693-9218265	HepG2	liver:	n/a	chr12:9217642-9217653
38	POLR2A	chr12:9216698-9218423	H1-hESC	embryonic stem cell:	n/a	n/a
39	CREB1	chr12:9216657-9219423	HepG2	liver:	n/a	n/a
40	POLR2A	chr12:9216623-9218202	Hela-S3	cervix:	n/a	n/a
41	MAX	chr12:9217250-9218295	H1-hESC	embryonic stem cell:	n/a	n/a
42	SMARCB1	chr12:9216813-9218222	Hela-S3	cervix:	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	chr12:9100379..9103293-chr12:9215519..9218225,4	MCF-7	breast:

No data

Variant related genes	Relation type
LINC00612	TF binding region
ENSG00000139187	Chromatin interaction
ENSG00000003056	Chromatin interaction
ENSG00000111752	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10743598	0.93[CHD][hapmap]
rs10771309	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];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842789	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842795	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842820	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10842845	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10842898	0.96[CEU][hapmap];0.81[CHB][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11048789	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs113973	0.93[CHD][hapmap]
rs1805651	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805652	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805653	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805654	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805655	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805656	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805657	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805658	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805659	0.82[CEU][hapmap];0.90[CHB][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805660	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805662	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];0.94[TSI][hapmap]
rs1805663	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.94[TSI][hapmap]
rs1805664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805666	0.90[CHB][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805667	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805678	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805681	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2193005	0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs226379	0.96[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs226380	0.93[CHD][hapmap]
rs226383	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs226384	0.91[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs226386	0.93[CHD][hapmap]
rs226388	0.93[CHD][hapmap]
rs226389	0.93[CHD][hapmap]
rs226393	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs226395	0.96[CEU][hapmap];0.90[CHB][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs226408	0.93[CHD][hapmap]
rs2300147	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2300148	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2377682	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6487574	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487581	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487585	0.81[CHB][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6487587	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs669	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7135781	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7299282	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7299600	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7309361	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7310089	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7310167	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310884	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7310921	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7955940	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];1.00[ASN][1000 genomes]
rs7965184	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7968640	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7976461	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs881376	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10771307	A2M	cis	Esophagus Mucosa	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9216200-9218400	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr12:9216600-9218400	Active TSS	H9 Cell Line	embryonic stem cell
3	chr12:9216600-9218400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr12:9216600-9218600	Active TSS	Brain Angular Gyrus	brain
5	chr12:9216600-9218600	Active TSS	NHLF	lung
6	chr12:9216800-9218400	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr12:9216800-9218400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:9216800-9218400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:9216800-9218400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:9216800-9218400	Active TSS	Brain Cingulate Gyrus	brain
11	chr12:9216800-9218400	Active TSS	Brain Hippocampus Middle	brain
12	chr12:9216800-9218400	Active TSS	Brain Substantia Nigra	brain
13	chr12:9216800-9218400	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr12:9216800-9218400	Active TSS	A549	lung
15	chr12:9216800-9218400	Active TSS	Osteobl	bone
16	chr12:9216800-9218600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr12:9216800-9218800	Active TSS	Fetal Lung	lung
18	chr12:9217000-9218400	Active TSS	HSMM	muscle
19	chr12:9217400-9223400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr12:9217600-9218400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr12:9217600-9223200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr12:9217800-9218400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
23	chr12:9217800-9218400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:9217800-9218400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr12:9217800-9218400	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr12:9217800-9218400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr12:9217800-9218400	Genic enhancers	Primary T cells fromperipheralblood	blood
28	chr12:9217800-9218400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:9217800-9218400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
30	chr12:9217800-9218400	Flanking Active TSS	Colonic Mucosa	Colon
31	chr12:9217800-9218400	Flanking Active TSS	Esophagus	oesophagus
32	chr12:9217800-9218400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
33	chr12:9217800-9218400	Flanking Active TSS	Left Ventricle	heart
34	chr12:9217800-9218400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr12:9217800-9218600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
36	chr12:9217800-9218600	Flanking Active TSS	Adipose Nuclei	Adipose
37	chr12:9217800-9218600	Flanking Active TSS	Liver	Liver
38	chr12:9217800-9218600	ZNF genes & repeats	Thymus	Thymus
39	chr12:9217800-9218800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
40	chr12:9217800-9218800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr12:9217800-9218800	Flanking Active TSS	Stomach Smooth Muscle	stomach
42	chr12:9217800-9219200	Enhancers	Gastric	stomach
43	chr12:9217800-9220400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr12:9217800-9225000	Weak transcription	Small Intestine	intestine
45	chr12:9217800-9234200	Weak transcription	Primary T cells from cord blood	blood
46	chr12:9218000-9218400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr12:9218000-9218400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr12:9218000-9218400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
49	chr12:9218000-9218400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr12:9218000-9218400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell

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