Variant report

Variant	rs6739171
Chromosome Location	chr2:37200033-37200034
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	chr2:37194252..37196693-chr2:37198973..37200836,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10084334	0.81[JPT][hapmap]
rs10167385	0.84[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs10176270	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10192867	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10207971	0.83[EUR][1000 genomes]
rs10865119	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11124556	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11682782	0.90[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs11684340	0.82[ASN][1000 genomes]
rs11895180	0.89[ASN][1000 genomes]
rs12104444	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12105601	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13394987	0.83[EUR][1000 genomes]
rs2013223	0.86[ASN][1000 genomes]
rs2110992	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2110998	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2247357	0.96[CEU][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2247935	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2287107	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs2287108	0.85[CEU][hapmap];0.94[CHB][hapmap];0.84[EUR][1000 genomes]
rs2372914	0.90[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap]
rs2540998	0.96[CEU][hapmap];0.89[CHB][hapmap];0.80[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.85[EUR][1000 genomes]
rs2541004	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2541007	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2691123	0.96[CEU][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2706809	0.81[EUR][1000 genomes]
rs3770774	0.84[CHB][hapmap];0.81[CHD][hapmap]
rs4255943	0.96[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4606899	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4670181	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4670642	0.81[ASN][1000 genomes]
rs4670643	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4670647	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4670650	0.82[EUR][1000 genomes]
rs58717433	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61380056	0.89[ASN][1000 genomes]
rs62133071	0.89[ASN][1000 genomes]
rs62133078	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6544050	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6709006	0.84[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs6712162	0.89[ASN][1000 genomes]
rs6733188	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9636429	0.89[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	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	nsv873879	chr2:37200033-37299145	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6739171	EIF2AK2	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37194400-37214200	Weak transcription	Pancreas	Pancrea
2	chr2:37194400-37229000	Weak transcription	Gastric	stomach
3	chr2:37194800-37206200	Weak transcription	Brain Germinal Matrix	brain
4	chr2:37194800-37211600	Weak transcription	HSMM	muscle
5	chr2:37194800-37226400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:37194800-37232400	Weak transcription	NHLF	lung
7	chr2:37195000-37206200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr2:37195000-37206400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:37195000-37206800	Weak transcription	Primary B cells from cord blood	blood
10	chr2:37195000-37206800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr2:37195000-37213800	Weak transcription	Right Ventricle	heart
12	chr2:37195000-37224200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr2:37195200-37202600	Weak transcription	Right Atrium	heart
14	chr2:37195200-37202600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr2:37195200-37205600	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr2:37195200-37206000	Weak transcription	Primary T cells from cord blood	blood
17	chr2:37195200-37206200	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr2:37195200-37206200	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr2:37195200-37206400	Weak transcription	Fetal Brain Female	brain
20	chr2:37195200-37206600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr2:37195200-37206800	Weak transcription	Adipose Nuclei	Adipose
22	chr2:37195200-37207600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr2:37195200-37211200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:37195200-37214000	Weak transcription	Brain Anterior Caudate	brain
25	chr2:37195200-37217400	Weak transcription	NHDF-Ad	bronchial
26	chr2:37195200-37225400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr2:37195200-37252800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr2:37195400-37206400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr2:37195400-37206600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr2:37195400-37207400	Weak transcription	GM12878-XiMat	blood
31	chr2:37195400-37207800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:37195400-37208600	Weak transcription	Osteobl	bone
33	chr2:37195400-37213800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr2:37195400-37215000	Weak transcription	Brain Hippocampus Middle	brain
35	chr2:37195400-37217600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr2:37195400-37227400	Weak transcription	A549	lung
37	chr2:37195400-37227600	Weak transcription	HUVEC	blood vessel
38	chr2:37195400-37248600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr2:37195600-37205800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:37195600-37206600	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:37195600-37215200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:37195600-37231400	Weak transcription	Brain Angular Gyrus	brain
43	chr2:37195800-37206000	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr2:37195800-37206400	Weak transcription	Fetal Muscle Leg	muscle
45	chr2:37195800-37207000	Weak transcription	Fetal Lung	lung
46	chr2:37195800-37208800	Weak transcription	Fetal Intestine Large	intestine
47	chr2:37195800-37229000	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr2:37196000-37206800	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr2:37196000-37206800	Weak transcription	Fetal Intestine Small	intestine
50	chr2:37196000-37207800	Weak transcription	Duodenum Mucosa	Duodenum

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