Variant report

Variant	rs3770774
Chromosome Location	chr2:37192495-37192496
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:37191677..37193362-chr2:37233119..37235779,2	K562	blood:
2	chr2:37186145..37190956-chr2:37191183..37194668,5	K562	blood:
3	chr2:37114816..37116390-chr2:37191550..37193356,2	MCF-7	breast:
4	chr2:37183661..37187179-chr2:37192061..37194972,3	MCF-7	breast:
5	chr2:37192443..37195662-chr2:37309226..37313144,4	K562	blood:
6	chr2:37170595..37172882-chr2:37190992..37193264,2	K562	blood:

Variant related genes	Relation type
ENSG00000008869	Chromatin interaction
ENSG00000252518	Chromatin interaction
ENSG00000152133	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10190027	0.87[ASN][1000 genomes]
rs10193295	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10490657	0.89[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs11124554	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11124555	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11124556	0.84[CHB][hapmap]
rs11695609	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12476515	0.92[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap]
rs13418962	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes]
rs17020071	0.95[JPT][hapmap]
rs17443495	0.89[CEU][hapmap];0.90[JPT][hapmap]
rs17497343	0.84[ASN][1000 genomes]
rs2003585	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2110992	0.80[ASN][1000 genomes]
rs2110994	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2245109	0.96[CEU][hapmap]
rs2252032	0.92[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap]
rs2372786	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2691106	0.92[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap]
rs2691112	0.81[EUR][1000 genomes]
rs2717493	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28527412	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3770781	0.82[CEU][hapmap]
rs3845778	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3845780	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]
rs4016033	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4016036	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4389320	0.89[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs45504994	0.84[EUR][1000 genomes]
rs4670637	0.84[ASN][1000 genomes]
rs4670638	0.90[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs4670642	0.81[ASN][1000 genomes]
rs4670643	0.80[ASN][1000 genomes]
rs57747847	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62133068	0.93[ASN][1000 genomes]
rs6752845	0.81[CEU][hapmap]
rs7561572	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7573966	0.96[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7588378	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7592902	0.82[EUR][1000 genomes]
rs7605601	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs888083	0.89[CEU][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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
6	esv3440334	chr2:37192273-37194821	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	esv3344704	chr2:37192448-37195146	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3770774	EIF2AK2	cis	cerebellum	SCAN
rs3770774	QPCT	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37179200-37192800	Weak transcription	Lung	lung
2	chr2:37186600-37192600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr2:37187400-37192600	Weak transcription	Fetal Muscle Trunk	muscle
4	chr2:37189200-37192600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:37190200-37192800	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr2:37191000-37192600	Enhancers	Primary B cells from peripheral blood	blood
7	chr2:37191000-37192600	Enhancers	Small Intestine	intestine
8	chr2:37191000-37192800	Enhancers	Spleen	Spleen
9	chr2:37191200-37192800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:37191200-37192800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:37191400-37192800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:37191600-37192600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr2:37191600-37192600	Enhancers	Primary T cells fromperipheralblood	blood
14	chr2:37191600-37192600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
15	chr2:37191600-37192800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:37191600-37192800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:37191600-37193200	Flanking Active TSS	Dnd41	blood
18	chr2:37191600-37194600	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr2:37191600-37194600	Active TSS	NHLF	lung
20	chr2:37191800-37192600	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr2:37191800-37192600	Enhancers	Primary B cells from cord blood	blood
22	chr2:37191800-37192600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr2:37191800-37192600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr2:37191800-37192600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
25	chr2:37191800-37192600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr2:37191800-37192600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:37191800-37192600	Enhancers	Brain Substantia Nigra	brain
28	chr2:37191800-37192600	Flanking Active TSS	A549	lung
29	chr2:37191800-37192800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
30	chr2:37191800-37192800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr2:37191800-37193000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr2:37191800-37193000	Active TSS	Right Atrium	heart
33	chr2:37191800-37193200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:37191800-37193200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:37191800-37193200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
36	chr2:37191800-37194000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr2:37191800-37194400	Active TSS	Esophagus	oesophagus
38	chr2:37191800-37194600	Active TSS	H9 Cell Line	embryonic stem cell
39	chr2:37191800-37194600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr2:37191800-37194600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr2:37191800-37194600	Active TSS	Left Ventricle	heart
42	chr2:37191800-37195000	Active TSS	NHDF-Ad	bronchial
43	chr2:37192000-37192600	Enhancers	Liver	Liver
44	chr2:37192000-37192600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr2:37192000-37192600	Flanking Active TSS	Stomach Smooth Muscle	stomach
46	chr2:37192000-37192800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr2:37192000-37192800	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr2:37192000-37192800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr2:37192000-37192800	Flanking Active TSS	Hela-S3	cervix
50	chr2:37192000-37192800	Flanking Active TSS	HUVEC	blood vessel

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