Variant report

Variant	rs3845780
Chromosome Location	chr2:37189296-37189297
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	chr2:37186145..37190956-chr2:37191183..37194668,5	K562	blood:

Variant related genes	Relation type
ENSG00000115808	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10190027	0.89[ASN][1000 genomes]
rs10193295	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10490657	1.00[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs11124554	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11124555	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11695609	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12476515	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs13418962	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17020071	1.00[JPT][hapmap]
rs17443495	0.89[CEU][hapmap];0.95[JPT][hapmap]
rs17497343	0.87[ASN][1000 genomes]
rs2003585	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2110994	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2245109	0.96[CEU][hapmap]
rs2252032	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs2372786	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2540998	0.84[CHB][hapmap]
rs2691106	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2691112	0.82[EUR][1000 genomes]
rs2717493	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28527412	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3770774	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3770781	0.82[CEU][hapmap]
rs3845778	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4016033	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4016036	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4389320	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs45504994	0.86[EUR][1000 genomes]
rs4670637	0.85[ASN][1000 genomes]
rs4670638	0.90[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs57747847	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62132550	0.80[EUR][1000 genomes]
rs62133068	0.96[ASN][1000 genomes]
rs6752845	0.81[CEU][hapmap]
rs7561572	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7573966	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7588378	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7592902	0.84[EUR][1000 genomes]
rs7605601	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs888083	0.89[CEU][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004483	chr2:36875235-37356812	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv535644	chr2:36875235-37356812	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv428395	chr2:36990348-37300352	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv456363	chr2:37109281-37235324	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv581470	chr2:37109281-37235324	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3845780	EIF2AK2	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37132400-37192400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr2:37134600-37192400	Weak transcription	Fetal Stomach	stomach
3	chr2:37143400-37191000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:37143800-37191800	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr2:37150200-37191800	Weak transcription	Fetal Thymus	thymus
6	chr2:37152400-37191800	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr2:37154600-37191800	Weak transcription	Fetal Intestine Large	intestine
8	chr2:37158200-37192000	Weak transcription	Ovary	ovary
9	chr2:37158600-37191800	Weak transcription	Fetal Lung	lung
10	chr2:37159000-37191800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr2:37165000-37190800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr2:37165600-37191800	Weak transcription	Fetal Intestine Small	intestine
13	chr2:37166600-37191600	Weak transcription	Dnd41	blood
14	chr2:37168600-37191800	Weak transcription	Thymus	Thymus
15	chr2:37176200-37191800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr2:37178600-37191200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr2:37178600-37191800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr2:37178800-37191600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr2:37178800-37191600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr2:37179000-37190200	Weak transcription	Placenta	Placenta
21	chr2:37179000-37190400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr2:37179000-37190800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr2:37179000-37191600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr2:37179200-37190800	Weak transcription	Gastric	stomach
25	chr2:37179200-37191200	Weak transcription	HSMMtube	muscle
26	chr2:37179200-37191600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:37179200-37191600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr2:37179200-37191600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:37179200-37191800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:37179200-37191800	Weak transcription	Fetal Muscle Leg	muscle
31	chr2:37179200-37191800	Weak transcription	Right Atrium	heart
32	chr2:37179200-37192000	Weak transcription	HSMM	muscle
33	chr2:37179200-37192800	Weak transcription	Lung	lung
34	chr2:37179400-37191400	Weak transcription	Primary T cells from cord blood	blood
35	chr2:37179400-37191800	Weak transcription	Osteobl	bone
36	chr2:37179600-37191800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr2:37179800-37190000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr2:37180000-37190200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr2:37180000-37191600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:37180000-37191600	Weak transcription	HUVEC	blood vessel
41	chr2:37180000-37192000	Weak transcription	Fetal Kidney	kidney
42	chr2:37180200-37190000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr2:37180200-37191800	Weak transcription	Brain Anterior Caudate	brain
44	chr2:37180400-37190200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr2:37180400-37190200	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr2:37180400-37191000	Weak transcription	Primary B cells from peripheral blood	blood
47	chr2:37180400-37191800	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr2:37180400-37191800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:37180400-37191800	Weak transcription	Primary B cells from cord blood	blood
50	chr2:37180600-37191800	Weak transcription	A549	lung

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