Variant report

Variant	rs7974396
Chromosome Location	chr12:9860697-9860698
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:9851492..9853618-chr12:9859229..9860813,2	K562	blood:
2	chr12:9786487..9787504-chr12:9860467..9861450,7	K562	blood:
3	chr12:9786489..9787540-chr12:9860512..9861375,9	MCF-7	breast:
4	chr12:9799365..9802259-chr12:9859677..9861748,3	MCF-7	breast:
5	chr12:9800782..9802831-chr12:9859086..9861954,2	MCF-7	breast:
6	chr12:9531253..9531816-chr12:9860516..9861214,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256442	Chromatin interaction
ENSG00000256594	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1008610	0.90[JPT][hapmap]
rs1044771	0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10466829	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs10492165	0.90[JPT][hapmap]
rs10492166	0.90[JPT][hapmap]
rs1056151	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10743823	0.85[JPT][hapmap]
rs10772046	0.85[ASN][1000 genomes]
rs10772062	0.84[ASN][1000 genomes]
rs10772070	0.82[ASN][1000 genomes]
rs10772071	0.82[ASN][1000 genomes]
rs10772072	0.82[ASN][1000 genomes]
rs10772073	0.82[ASN][1000 genomes]
rs10772074	0.81[ASN][1000 genomes]
rs10772079	0.81[ASN][1000 genomes]
rs10772085	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs10772087	0.89[JPT][hapmap]
rs10772102	0.90[JPT][hapmap]
rs10844456	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10844468	0.85[ASN][1000 genomes]
rs10844472	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10844503	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10844537	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10844562	0.85[ASN][1000 genomes]
rs10844569	0.81[ASN][1000 genomes]
rs10844609	0.81[ASN][1000 genomes]
rs10844615	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs10844617	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs10844620	0.89[JPT][hapmap]
rs10844636	0.89[JPT][hapmap]
rs10844638	0.89[JPT][hapmap]
rs10844657	0.90[JPT][hapmap]
rs10844706	0.84[JPT][hapmap]
rs11052372	0.89[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs11052423	0.89[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs11052426	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11052497	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11052552	0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11052582	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052604	0.87[ASN][1000 genomes]
rs11052710	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs11052717	0.81[ASN][1000 genomes]
rs11052877	0.89[JPT][hapmap]
rs12227655	0.89[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs12228641	0.84[ASN][1000 genomes]
rs12424826	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12427310	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12582584	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1560011	0.94[CHB][hapmap];0.83[ASN][1000 genomes]
rs17806710	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1985788	0.91[ASN][1000 genomes]
rs2012643	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2058560	0.81[ASN][1000 genomes]
rs2080206	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2080211	0.84[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs2098298	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2114870	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs2114871	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2192437	0.80[ASN][1000 genomes]
rs2268146	0.83[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2401390	0.81[ASN][1000 genomes]
rs2401391	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs2401393	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs2401394	0.80[ASN][1000 genomes]
rs2401395	0.80[ASN][1000 genomes]
rs2894	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2895988	1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3764021	0.89[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3764022	0.89[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs4763283	0.92[ASN][1000 genomes]
rs4763839	0.88[ASN][1000 genomes]
rs4763840	0.84[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs61915472	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61915473	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7296241	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7306304	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs7306557	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs7310460	0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs741199	0.81[ASN][1000 genomes]
rs741200	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7960328	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7964018	0.96[ASN][1000 genomes]
rs7968401	0.84[ASN][1000 genomes]
rs7970116	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs7973535	0.80[ASN][1000 genomes]
rs7973638	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs7976584	0.80[ASN][1000 genomes]
rs7977720	0.86[ASN][1000 genomes]
rs7977940	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs917911	0.84[JPT][hapmap]
rs917913	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332411	0.88[CHB][hapmap];0.86[EUR][1000 genomes];0.82[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	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
2	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv983235	chr12:9852218-9893776	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv2757490	chr12:9855958-9888553	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7974396	CLECL1	Cis_1M	lymphoblastoid	RTeQTL
rs7974396	CLECL1	cis	Nerve Tibial	GTEx
rs7974396	CLEC2D	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9840600-9864600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:9841800-9863200	Weak transcription	HSMMtube	muscle
3	chr12:9855600-9862800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr12:9857600-9861600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr12:9858000-9872200	Enhancers	Primary B cells from peripheral blood	blood
6	chr12:9858400-9861000	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr12:9858600-9860800	Enhancers	Thymus	Thymus
8	chr12:9858600-9861400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr12:9858600-9861400	Enhancers	Dnd41	blood
10	chr12:9858800-9861400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
11	chr12:9859000-9870200	Enhancers	Primary B cells from cord blood	blood
12	chr12:9859400-9860800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:9860000-9860800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
14	chr12:9860000-9860800	Enhancers	Esophagus	oesophagus
15	chr12:9860000-9860800	Enhancers	Left Ventricle	heart
16	chr12:9860000-9860800	Enhancers	Spleen	Spleen
17	chr12:9860000-9860800	Enhancers	HMEC	breast
18	chr12:9860000-9861000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr12:9860000-9861000	Enhancers	Fetal Thymus	thymus
20	chr12:9860000-9861000	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr12:9860000-9861200	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr12:9860000-9861400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:9860200-9860800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
24	chr12:9860200-9861000	Flanking Active TSS	Primary T cells from cord blood	blood
25	chr12:9860200-9861000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
26	chr12:9860400-9860800	Enhancers	Pancreas	Pancrea
27	chr12:9860400-9860800	Enhancers	A549	lung
28	chr12:9860400-9861000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
29	chr12:9860400-9861000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr12:9860400-9861000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr12:9860400-9861000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr12:9860400-9861200	Enhancers	K562	blood
33	chr12:9860400-9861800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr12:9860400-9861800	Flanking Active TSS	GM12878-XiMat	blood
35	chr12:9860600-9860800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr12:9860600-9860800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
37	chr12:9860600-9860800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr12:9860600-9860800	Enhancers	Colonic Mucosa	Colon
39	chr12:9860600-9860800	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr12:9860600-9860800	ZNF genes & repeats	Lung	lung
41	chr12:9860600-9860800	Flanking Active TSS	HepG2	liver
42	chr12:9860600-9861000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
43	chr12:9860600-9861000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
44	chr12:9860600-9861000	Enhancers	Adipose Nuclei	Adipose
45	chr12:9860600-9861000	Enhancers	Liver	Liver
46	chr12:9860600-9861000	Enhancers	Placenta	Placenta
47	chr12:9860600-9861000	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr12:9860600-9861200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr12:9860600-9861200	Enhancers	Right Ventricle	heart
50	chr12:9860600-9861200	Enhancers	Stomach Mucosa	stomach

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