Variant report

Variant	rs12694858
Chromosome Location	chr2:231252584-231252585
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	chr2:231250673..231252951-chr2:231254109..231256319,2	K562	blood:
2	chr2:231245270..231247001-chr2:231250596..231253585,2	K562	blood:

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10165727	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10181582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10181779	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10184953	0.81[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10189380	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10194531	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10198517	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11686704	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12694850	0.94[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12694851	1.00[CEU][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12694853	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12694854	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12694855	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12694856	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12694859	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12694860	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12694862	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12694863	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12994857	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13012177	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13012615	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13025664	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13028885	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13383901	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13383916	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13383946	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13384148	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13384237	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13384350	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13390006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13397699	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13409103	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1579395	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1609427	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1816208	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap]
rs1820551	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1863672	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1968342	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2894710	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35935297	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3856528	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4364013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4577270	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4638786	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6709797	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6710190	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6738146	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6738151	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7585740	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7586155	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9288667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	esv3417154	chr2:231159789-231258938	Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv3348338	chr2:231160124-231259498	Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv875945	chr2:231172642-231267925	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv869708	chr2:231173700-231267616	Genic enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1004183	chr2:231174420-231258603	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	esv3486129	chr2:231175581-231265831	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv3486131	chr2:231175581-231265831	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1013738	chr2:231176856-231258603	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv584667	chr2:231177822-231258450	Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv460119	chr2:231178876-231258450	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv584668	chr2:231178876-231258450	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	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
14	nsv1001929	chr2:231179884-231258603	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv1006206	chr2:231179884-231268938	Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv584669	chr2:231183321-231258150	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	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
18	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12694858	LOC93349	Cis_1M	lymphoblastoid	RTeQTL
rs12694858	LOC93349	cis	multi-tissue	Pritchard

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231212800-231253600	Weak transcription	Gastric	stomach
2	chr2:231212800-231253600	Weak transcription	HMEC	breast
3	chr2:231212800-231259200	Weak transcription	Small Intestine	intestine
4	chr2:231212800-231262400	Weak transcription	K562	blood
5	chr2:231220000-231275800	Weak transcription	Stomach Mucosa	stomach
6	chr2:231222200-231253400	Weak transcription	Colonic Mucosa	Colon
7	chr2:231222200-231273200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr2:231223200-231253600	Weak transcription	NHLF	lung
9	chr2:231223400-231257800	Weak transcription	NH-A	brain
10	chr2:231223600-231263600	Weak transcription	Fetal Kidney	kidney
11	chr2:231224200-231254000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:231225200-231268000	Weak transcription	Colon Smooth Muscle	Colon
13	chr2:231226600-231253800	Weak transcription	Fetal Stomach	stomach
14	chr2:231226800-231253600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:231226800-231253600	Weak transcription	Pancreas	Pancrea
16	chr2:231228800-231260000	Strong transcription	Primary B cells from peripheral blood	blood
17	chr2:231228800-231275600	Weak transcription	Psoas Muscle	Psoas
18	chr2:231232200-231260400	Weak transcription	Fetal Lung	lung
19	chr2:231234200-231253600	Weak transcription	Esophagus	oesophagus
20	chr2:231234200-231274400	Weak transcription	Brain Hippocampus Middle	brain
21	chr2:231234400-231259400	Weak transcription	Fetal Intestine Small	intestine
22	chr2:231236800-231260000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:231237000-231253600	Weak transcription	GM12878-XiMat	blood
24	chr2:231237000-231264800	Weak transcription	HepG2	liver
25	chr2:231237200-231264800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:231238000-231253800	Weak transcription	Fetal Muscle Leg	muscle
27	chr2:231238200-231253600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr2:231238200-231253600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:231238200-231257600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:231238600-231253600	Weak transcription	Left Ventricle	heart
31	chr2:231240000-231259600	Strong transcription	Primary B cells from cord blood	blood
32	chr2:231244600-231259400	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr2:231244600-231260000	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr2:231244800-231260000	Strong transcription	Primary T cells from cord blood	blood
35	chr2:231244800-231260000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr2:231245000-231260400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr2:231245200-231265600	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr2:231245400-231260400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr2:231245800-231266000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr2:231246200-231253600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr2:231246400-231260200	Strong transcription	Placenta	Placenta
42	chr2:231247600-231258800	Strong transcription	Primary hematopoietic stem cells	blood
43	chr2:231247600-231260000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr2:231248000-231254800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr2:231248000-231260000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:231248000-231260000	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr2:231248000-231262600	Strong transcription	Liver	Liver
48	chr2:231248000-231265400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr2:231248000-231274600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr2:231248200-231255000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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