Variant report

Variant	rs2888657
Chromosome Location	chr2:40375249-40375250
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10183046	0.89[JPT][hapmap]
rs10490206	0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11676744	0.81[CEU][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11680622	0.89[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11687766	0.89[CEU][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12464756	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12466767	0.89[CEU][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12470980	0.85[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12478057	0.85[CEU][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12712683	0.89[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13005439	0.83[JPT][hapmap]
rs1428566	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs1428567	0.81[CEU][hapmap]
rs1428568	0.81[CEU][hapmap]
rs17501526	0.89[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17559580	0.85[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17559651	0.85[CEU][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2005886	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2072531	0.91[TSI][hapmap]
rs2072532	0.89[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2110926	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2373791	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2373792	0.89[CEU][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4952354	0.85[CEU][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes]
rs4952498	0.81[EUR][1000 genomes]
rs5542	0.84[CHD][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap]
rs5551	0.81[CEU][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes]
rs56090875	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62150869	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62150874	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6742885	0.89[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs929642	0.85[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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
10	nsv873907	chr2:40349094-40381369	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv1005758	chr2:40349403-40381369	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2888657	ABCG5	cis	parietal	SCAN
rs2888657	SOS1	cis	parietal	SCAN

Chromatin state (count:48 , 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	chr2:40364200-40377400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr2:40364400-40383800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:40364600-40387000	Weak transcription	Placenta	Placenta
10	chr2:40364800-40380400	Weak transcription	Fetal Intestine Small	intestine
11	chr2:40365200-40396200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr2:40366600-40403000	Weak transcription	Brain Germinal Matrix	brain
13	chr2:40366800-40376800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:40366800-40382800	Weak transcription	Right Ventricle	heart
15	chr2:40366800-40383000	Weak transcription	Aorta	Aorta
16	chr2:40366800-40387200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr2:40366800-40391800	Weak transcription	Fetal Muscle Trunk	muscle
18	chr2:40367000-40382800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:40367000-40384400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr2:40368400-40377400	Weak transcription	Brain Anterior Caudate	brain
21	chr2:40368600-40383000	Weak transcription	Fetal Brain Female	brain
22	chr2:40368600-40383800	Weak transcription	Osteobl	bone
23	chr2:40368800-40376800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr2:40369000-40381000	Weak transcription	Colon Smooth Muscle	Colon
25	chr2:40369200-40382800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr2:40369600-40391600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr2:40370600-40376800	Weak transcription	Fetal Brain Male	brain
28	chr2:40371400-40375400	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr2:40371800-40377400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr2:40371800-40391800	Weak transcription	NHDF-Ad	bronchial
31	chr2:40372000-40378400	Strong transcription	Dnd41	blood
32	chr2:40372400-40376600	Weak transcription	Fetal Thymus	thymus
33	chr2:40373000-40377000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr2:40373000-40377200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:40374000-40375600	Enhancers	HSMMtube	muscle
36	chr2:40374000-40384400	Weak transcription	Fetal Stomach	stomach
37	chr2:40374400-40377800	Strong transcription	Stomach Smooth Muscle	stomach
38	chr2:40374400-40378600	Genic enhancers	Fetal Heart	heart
39	chr2:40374600-40375600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:40374800-40375600	Genic enhancers	HSMM	muscle
41	chr2:40374800-40375800	Weak transcription	Left Ventricle	heart
42	chr2:40374800-40377000	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr2:40374800-40377200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr2:40375000-40375400	Weak transcription	Fetal Muscle Leg	muscle
45	chr2:40375000-40375400	Genic enhancers	Monocytes-CD14+_RO01746	blood
46	chr2:40375000-40375600	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr2:40375000-40377200	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr2:40375200-40376400	Enhancers	Primary monocytes fromperipheralblood	blood

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