Variant report

Variant	rs10843958
Chromosome Location	chr12:31647813-31647814
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:31645308..31649621-chr12:31742506..31745309,6	MCF-7	breast:
2	chr12:31645681..31648505-chr12:31649831..31652317,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255867	Chromatin interaction
ENSG00000170456	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10743757	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10743759	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10771827	0.86[EUR][1000 genomes]
rs10771828	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10771832	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10771838	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10771843	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10771844	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10771845	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10771846	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10843942	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10843959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10843963	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11051418	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11051435	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11051437	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11051439	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11051441	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11615961	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1259355	0.89[ASN][1000 genomes]
rs1259428	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1259432	0.93[ASN][1000 genomes]
rs1271128	0.88[ASN][1000 genomes]
rs1469673	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1996693	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2116704	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2352048	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2617190	0.84[EUR][1000 genomes]
rs2682697	0.82[EUR][1000 genomes]
rs2682700	0.83[EUR][1000 genomes]
rs2888762	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3803113	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3844573	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3850965	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3853626	0.82[EUR][1000 genomes]
rs3898368	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4482118	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4930980	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4931488	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4931501	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931506	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4931507	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6416254	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6487989	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6487992	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487996	0.87[EUR][1000 genomes]
rs66521153	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs708209	0.83[EUR][1000 genomes]
rs7133082	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7134365	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7135856	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7136476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7136943	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137406	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7294574	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7302698	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7303447	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7303848	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7307593	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7307616	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7313118	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313158	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7313689	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7314417	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793146	0.84[EUR][1000 genomes]
rs793154	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs793157	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs793180	0.84[EUR][1000 genomes]
rs793184	0.84[EUR][1000 genomes]
rs7954023	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7954595	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7957026	0.87[EUR][1000 genomes]
rs7959877	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7962896	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7963161	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7967832	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7968291	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7974437	0.87[ASN][1000 genomes]
rs7975761	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7976644	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7977453	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9738834	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS 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	71 gene(s)	inside rSNPs	diseases
3	esv2751046	chr12:31174233-31684733	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv832364	chr12:31467990-31648144	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	esv1836923	chr12:31539122-31761172	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv898965	chr12:31631819-31771689	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv832365	chr12:31642811-31808532	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31577800-31649400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr12:31583400-31662000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:31594400-31648400	Weak transcription	Small Intestine	intestine
4	chr12:31628800-31655800	Weak transcription	Gastric	stomach
5	chr12:31630400-31655000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr12:31633000-31648800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr12:31633000-31651600	Weak transcription	Fetal Muscle Leg	muscle
8	chr12:31633000-31652400	Weak transcription	Fetal Brain Female	brain
9	chr12:31633200-31649200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr12:31633200-31649600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr12:31633200-31652200	Weak transcription	Adipose Nuclei	Adipose
12	chr12:31636200-31663000	Weak transcription	Aorta	Aorta
13	chr12:31637600-31648800	Weak transcription	Fetal Stomach	stomach
14	chr12:31639000-31655800	Weak transcription	Left Ventricle	heart
15	chr12:31640600-31650400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr12:31641800-31649000	Strong transcription	Primary B cells from cord blood	blood
17	chr12:31642600-31670000	Weak transcription	Fetal Lung	lung
18	chr12:31643600-31648400	Enhancers	Hela-S3	cervix
19	chr12:31643600-31658800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr12:31644000-31648000	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr12:31644000-31648200	Strong transcription	HepG2	liver
22	chr12:31644400-31659400	Weak transcription	Pancreas	Pancrea
23	chr12:31644800-31650000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr12:31645200-31650200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr12:31645400-31648400	Weak transcription	Stomach Mucosa	stomach
26	chr12:31645400-31648800	Strong transcription	Fetal Intestine Large	intestine
27	chr12:31645400-31650000	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr12:31645600-31658000	Weak transcription	Fetal Intestine Small	intestine
29	chr12:31645800-31649000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:31645800-31649200	Weak transcription	NHDF-Ad	bronchial
31	chr12:31645800-31649400	Weak transcription	NHLF	lung
32	chr12:31645800-31650200	Weak transcription	Osteobl	bone
33	chr12:31645800-31651000	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr12:31645800-31651000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr12:31646000-31649000	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr12:31646000-31649200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr12:31646000-31649800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr12:31646000-31650600	Weak transcription	Right Ventricle	heart
39	chr12:31646000-31651000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr12:31646000-31652000	Weak transcription	Brain Germinal Matrix	brain
41	chr12:31646000-31652400	Weak transcription	Fetal Kidney	kidney
42	chr12:31646000-31652600	Weak transcription	Brain Hippocampus Middle	brain
43	chr12:31646000-31659400	Weak transcription	NH-A	brain
44	chr12:31646000-31659800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr12:31646200-31648800	Weak transcription	Brain Anterior Caudate	brain
46	chr12:31646200-31649000	Weak transcription	HSMMtube	muscle
47	chr12:31646200-31650200	Weak transcription	Fetal Heart	heart
48	chr12:31646200-31650600	Weak transcription	HSMM	muscle
49	chr12:31646200-31651000	Weak transcription	Colon Smooth Muscle	Colon
50	chr12:31646200-31651200	Weak transcription	HUVEC	blood vessel

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