Variant report

Variant	rs12694863
Chromosome Location	chr2:231273785-231273786
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	chr2:231273497..231275007-chr2:231279310..231281217,2	MCF-7	breast:
2	chr2:231211181..231213107-chr2:231272080..231274624,2	K562	blood:

Variant related genes	Relation type
ENSG00000067066	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10165727	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10181582	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10181779	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10184953	0.95[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10189380	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10194531	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10198517	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11686704	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12694850	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12694851	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12694853	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12694854	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12694855	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12694856	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12694858	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12694859	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12694860	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12694862	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12994857	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13012177	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13012615	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13025664	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13028885	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13383901	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13383916	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13383946	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13384148	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13384237	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13384350	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13390006	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13397699	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13409103	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1579395	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1609427	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1816208	1.00[CEU][hapmap]
rs1820551	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1863672	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1968342	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2894710	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35935297	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3856528	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4364013	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4577270	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4638786	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6709797	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6710190	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6738146	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6738151	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7585740	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7586155	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9288667	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv2751844	chr2:231179495-231280495	Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv875946	chr2:231184106-231277567	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv875947	chr2:231190446-231281286	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv521344	chr2:231267925-231281286	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv584671	chr2:231273229-231284556	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12694863	LOC93349	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231220000-231275800	Weak transcription	Stomach Mucosa	stomach
2	chr2:231228800-231275600	Weak transcription	Psoas Muscle	Psoas
3	chr2:231234200-231274400	Weak transcription	Brain Hippocampus Middle	brain
4	chr2:231248000-231274600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:231255200-231275600	Weak transcription	HMEC	breast
6	chr2:231258800-231275600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:231260200-231275400	Weak transcription	Small Intestine	intestine
8	chr2:231264600-231275800	Weak transcription	K562	blood
9	chr2:231265000-231275600	Weak transcription	Fetal Heart	heart
10	chr2:231265400-231275400	Weak transcription	HepG2	liver
11	chr2:231265600-231275400	Weak transcription	Colonic Mucosa	Colon
12	chr2:231265600-231275400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr2:231265600-231275600	Weak transcription	Fetal Intestine Large	intestine
14	chr2:231267600-231275800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr2:231268600-231275200	Weak transcription	Colon Smooth Muscle	Colon
16	chr2:231268800-231273800	Weak transcription	Thymus	Thymus
17	chr2:231268800-231275400	Weak transcription	Fetal Thymus	thymus
18	chr2:231268800-231275600	Weak transcription	Dnd41	blood
19	chr2:231269000-231275200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr2:231269000-231275200	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr2:231269200-231275600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr2:231269200-231275800	Weak transcription	Fetal Intestine Small	intestine
23	chr2:231269800-231273800	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr2:231269800-231274800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr2:231269800-231275400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr2:231269800-231275600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr2:231270000-231276000	Enhancers	HUVEC	blood vessel
28	chr2:231270600-231273800	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr2:231270600-231275600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr2:231270600-231275800	Weak transcription	HSMMtube	muscle
31	chr2:231270800-231274400	Weak transcription	GM12878-XiMat	blood
32	chr2:231270800-231275600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:231271400-231273800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr2:231271800-231273800	Weak transcription	Primary B cells from peripheral blood	blood
35	chr2:231271800-231275400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr2:231272000-231275600	Weak transcription	Primary T cells from cord blood	blood
37	chr2:231272000-231275600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr2:231272000-231275800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr2:231272400-231274600	Enhancers	Right Atrium	heart
40	chr2:231272600-231273800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr2:231272600-231274000	Enhancers	NHLF	lung
42	chr2:231272600-231274200	Enhancers	NHDF-Ad	bronchial
43	chr2:231272600-231274400	Weak transcription	Primary B cells from cord blood	blood
44	chr2:231272600-231275600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:231272800-231273800	Enhancers	Osteobl	bone
46	chr2:231272800-231274000	Enhancers	NHEK	skin
47	chr2:231272800-231274200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:231272800-231274200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr2:231272800-231275400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr2:231272800-231275600	Enhancers	Primary T helper cells fromperipheralblood	blood

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