Variant report

Variant	rs395404
Chromosome Location	chr2:40382626-40382627
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10205502	0.83[CHD][hapmap]
rs11688023	1.00[CHB][hapmap]
rs11692455	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13425134	0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1366423	0.80[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2110923	0.90[CHD][hapmap]
rs2110925	0.90[CHD][hapmap]
rs373606	0.82[JPT][hapmap]
rs374943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs375357	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs391984	0.81[JPT][hapmap]
rs394157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs397427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs406880	0.86[JPT][hapmap]
rs407889	0.82[JPT][hapmap]
rs414648	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs414720	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs417614	0.83[CHD][hapmap]
rs418780	0.82[JPT][hapmap]
rs423573	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs429602	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs429648	0.88[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs432188	0.88[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs435403	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs435923	0.86[CHD][hapmap]
rs435981	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs441413	0.82[JPT][hapmap]
rs445972	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs452369	0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs453970	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4952490	0.83[CHD][hapmap]
rs4952491	0.83[CHD][hapmap]
rs4952499	0.94[ASN][1000 genomes]
rs507705	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs519147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs987330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv873902	chr2:40231282-40466268	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1004092	chr2:40264608-40451701	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1000572	chr2:40271958-40458911	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv535654	chr2:40271958-40458911	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv581502	chr2:40273903-40459645	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv873903	chr2:40285145-40382712	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv873904	chr2:40292289-40466268	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv873906	chr2:40341847-40385045	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40355400-40383800	Weak transcription	Small Intestine	intestine
2	chr2:40357800-40406400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:40358000-40392200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr2:40358200-40392200	Weak transcription	NHLF	lung
5	chr2:40358800-40389200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:40359000-40387400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:40364400-40383800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:40364600-40387000	Weak transcription	Placenta	Placenta
9	chr2:40365200-40396200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:40366600-40403000	Weak transcription	Brain Germinal Matrix	brain
11	chr2:40366800-40382800	Weak transcription	Right Ventricle	heart
12	chr2:40366800-40383000	Weak transcription	Aorta	Aorta
13	chr2:40366800-40387200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr2:40366800-40391800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr2:40367000-40382800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:40367000-40384400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr2:40368600-40383000	Weak transcription	Fetal Brain Female	brain
18	chr2:40368600-40383800	Weak transcription	Osteobl	bone
19	chr2:40369200-40382800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr2:40369600-40391600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr2:40371800-40391800	Weak transcription	NHDF-Ad	bronchial
22	chr2:40374000-40384400	Weak transcription	Fetal Stomach	stomach
23	chr2:40375600-40384600	Weak transcription	Fetal Muscle Leg	muscle
24	chr2:40375600-40401800	Weak transcription	HSMMtube	muscle
25	chr2:40376200-40387000	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr2:40376800-40394200	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr2:40377600-40383000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:40377600-40383800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:40377600-40386200	Weak transcription	Fetal Brain Male	brain
30	chr2:40377800-40382800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:40377800-40383000	Weak transcription	Stomach Smooth Muscle	stomach
32	chr2:40378000-40391200	Weak transcription	Brain Anterior Caudate	brain
33	chr2:40378000-40391200	Weak transcription	Fetal Thymus	thymus
34	chr2:40378000-40399000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr2:40378200-40392000	Weak transcription	Gastric	stomach
36	chr2:40379200-40393400	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr2:40381000-40384800	Strong transcription	Colon Smooth Muscle	Colon
38	chr2:40381200-40382800	Weak transcription	HSMM	muscle
39	chr2:40381200-40391800	Weak transcription	Adipose Nuclei	Adipose
40	chr2:40381400-40385600	Weak transcription	Fetal Intestine Large	intestine
41	chr2:40381400-40390200	Weak transcription	Fetal Intestine Small	intestine
42	chr2:40381600-40398800	Weak transcription	Brain Angular Gyrus	brain
43	chr2:40381800-40395200	Weak transcription	Spleen	Spleen
44	chr2:40382200-40385400	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr2:40382400-40386400	Weak transcription	HMEC	breast
46	chr2:40382400-40392800	Strong transcription	Dnd41	blood
47	chr2:40382600-40384200	Strong transcription	Fetal Kidney	kidney
48	chr2:40382600-40385000	Genic enhancers	Fetal Heart	heart
49	chr2:40382600-40391800	Strong transcription	Left Ventricle	heart

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