Variant report

Variant	rs1168669
Chromosome Location	chr12:122228694-122228695
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:122134034..122138136-chr12:122226162..122228726,3	MCF-7	breast:
2	chr12:122188669..122193873-chr12:122227176..122233304,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188735	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1004390	0.91[EUR][1000 genomes]
rs11043202	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043203	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043207	0.80[EUR][1000 genomes]
rs1168663	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1168664	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1168665	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1168666	0.94[EUR][1000 genomes]
rs1168668	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168671	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1168672	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168673	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12307227	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12313997	0.89[ASN][1000 genomes]
rs12314801	0.89[ASN][1000 genomes]
rs12820413	0.82[ASN][1000 genomes]
rs12823194	0.85[EUR][1000 genomes]
rs1667578	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1667579	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1795965	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1795966	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2019561	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2019562	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2122266	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2707057	0.82[ASN][1000 genomes]
rs2707066	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2707067	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712852	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7957564	0.91[EUR][1000 genomes]
rs7974348	0.92[EUR][1000 genomes]
rs895951	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895952	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895953	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs895954	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs895957	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs921286	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs921287	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs930665	0.93[EUR][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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv899566	chr12:122167095-122265106	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
3	nsv899567	chr12:122203680-122281575	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv984477	chr12:122226309-122271532	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1168669	AC084018.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122206400-122230600	Weak transcription	Brain Angular Gyrus	brain
2	chr12:122211600-122231200	Weak transcription	Brain Hippocampus Middle	brain
3	chr12:122211800-122231600	Weak transcription	Brain Substantia Nigra	brain
4	chr12:122217800-122230400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr12:122219000-122229800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr12:122219200-122230600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr12:122219200-122230600	Weak transcription	Fetal Brain Female	brain
8	chr12:122219600-122230800	Weak transcription	Brain Germinal Matrix	brain
9	chr12:122220400-122230400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr12:122220400-122230600	Weak transcription	Brain Anterior Caudate	brain
11	chr12:122220600-122230400	Weak transcription	Colon Smooth Muscle	Colon
12	chr12:122220600-122230400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr12:122220800-122229600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr12:122221200-122230600	Weak transcription	Right Atrium	heart
15	chr12:122223200-122231400	Weak transcription	HSMM	muscle
16	chr12:122224000-122229400	Genic enhancers	Fetal Intestine Small	intestine
17	chr12:122224200-122228800	Genic enhancers	Fetal Intestine Large	intestine
18	chr12:122224200-122229000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr12:122224600-122231200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr12:122224800-122231000	Weak transcription	Osteobl	bone
21	chr12:122225200-122229400	Weak transcription	HMEC	breast
22	chr12:122225200-122229600	Weak transcription	NHEK	skin
23	chr12:122225200-122231400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr12:122225400-122229600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr12:122225400-122229600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr12:122225400-122230000	Enhancers	Spleen	Spleen
27	chr12:122225400-122231000	Weak transcription	Pancreas	Pancrea
28	chr12:122225600-122230400	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr12:122225800-122228800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr12:122225800-122233200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr12:122226000-122228800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr12:122226000-122228800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr12:122226000-122228800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr12:122226000-122228800	Flanking Active TSS	GM12878-XiMat	blood
35	chr12:122226000-122229600	Transcr. at gene 5' and 3'	Hela-S3	cervix
36	chr12:122226200-122228800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr12:122226200-122228800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
38	chr12:122226200-122228800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
39	chr12:122226200-122229400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:122226400-122228800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr12:122226400-122229400	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr12:122226600-122228800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr12:122226600-122228800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
44	chr12:122226600-122229400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:122226800-122228800	Flanking Active TSS	Colonic Mucosa	Colon
46	chr12:122226800-122229400	Weak transcription	HSMMtube	muscle
47	chr12:122227000-122229400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
48	chr12:122227200-122231600	Weak transcription	K562	blood
49	chr12:122227400-122229000	Enhancers	HUVEC	blood vessel
50	chr12:122227400-122229600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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