Variant report

Variant	rs2715933
Chromosome Location	chr2:160877502-160877503
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10192293	1.00[YRI][hapmap]
rs1039930	0.90[ASN][1000 genomes]
rs1039931	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10454740	1.00[YRI][hapmap]
rs10929961	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11887337	1.00[YRI][hapmap]
rs13009425	1.00[JPT][hapmap]
rs13025687	1.00[JPT][hapmap]
rs13032589	1.00[YRI][hapmap]
rs13394776	1.00[YRI][hapmap]
rs13427061	1.00[YRI][hapmap]
rs1397709	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1397713	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1457240	1.00[YRI][hapmap]
rs1471121	1.00[YRI][hapmap]
rs1511213	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1511215	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1543063	0.82[ASN][1000 genomes]
rs1567537	0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17241394	0.84[JPT][hapmap]
rs1858295	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061288	1.00[YRI][hapmap]
rs2357773	1.00[YRI][hapmap]
rs2465668	0.84[ASN][1000 genomes]
rs2666995	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2666996	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2666997	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2666998	0.84[ASN][1000 genomes]
rs2667000	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2667002	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2667006	0.87[ASN][1000 genomes]
rs2667007	0.87[ASN][1000 genomes]
rs2667009	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2667010	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2667011	0.88[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2667013	0.87[ASN][1000 genomes]
rs2667014	0.88[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2667017	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2667019	0.90[ASN][1000 genomes]
rs2667023	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2667025	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2667033	1.00[YRI][hapmap]
rs2667038	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2667040	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs2667041	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2667042	0.94[ASN][1000 genomes]
rs2667043	0.94[ASN][1000 genomes]
rs2667044	0.94[ASN][1000 genomes]
rs2667045	0.91[ASN][1000 genomes]
rs2715914	0.86[ASN][1000 genomes]
rs2715916	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2715918	0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2715919	0.84[ASN][1000 genomes]
rs2715920	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2715921	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2715923	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2715931	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2715932	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2715934	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2715935	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2715936	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2715937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2715938	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2715942	0.94[ASN][1000 genomes]
rs2715944	0.94[ASN][1000 genomes]
rs2715945	0.90[ASN][1000 genomes]
rs2715946	0.81[ASN][1000 genomes]
rs2715947	0.87[ASN][1000 genomes]
rs2715948	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2715949	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2715950	0.88[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2925756	1.00[YRI][hapmap]
rs2925763	1.00[YRI][hapmap]
rs3106306	0.93[ASN][1000 genomes]
rs3792185	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792186	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233679	1.00[YRI][hapmap]
rs4401175	0.84[ASN][1000 genomes]
rs4665155	1.00[YRI][hapmap]
rs6432593	1.00[YRI][hapmap]
rs6432603	1.00[YRI][hapmap]
rs6704861	0.93[ASN][1000 genomes]
rs6729540	1.00[YRI][hapmap]
rs7573748	1.00[JPT][hapmap]
rs7583743	1.00[YRI][hapmap]
rs7590560	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7601113	1.00[YRI][hapmap]
rs7608152	1.00[YRI][hapmap]
rs883423	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs996112	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875345	chr2:160805582-160885442	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv2997	chr2:160841578-160886352	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2715933	CYTIP	cis	parietal	SCAN
rs2715933	LY75	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:160828600-160907200	Weak transcription	Small Intestine	intestine
2	chr2:160839800-160885000	Weak transcription	HUVEC	blood vessel
3	chr2:160853800-160879400	Weak transcription	NHEK	skin
4	chr2:160854000-160884600	Weak transcription	Fetal Lung	lung
5	chr2:160854400-160880200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr2:160854800-160880800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:160855600-160879000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr2:160855600-160884600	Weak transcription	Osteobl	bone
9	chr2:160861600-160878400	Weak transcription	NH-A	brain
10	chr2:160861600-160880600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:160861600-160880600	Weak transcription	Fetal Stomach	stomach
12	chr2:160861600-160884800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr2:160861800-160878000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:160862800-160879600	Weak transcription	Right Ventricle	heart
15	chr2:160862800-160880400	Weak transcription	Esophagus	oesophagus
16	chr2:160862800-160899600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr2:160864000-160880600	Weak transcription	Spleen	Spleen
18	chr2:160864400-160885200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr2:160865200-160883200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:160867600-160878600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr2:160867600-160893800	Weak transcription	HMEC	breast
22	chr2:160868800-160878800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:160869000-160878600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr2:160869000-160878600	Weak transcription	NHDF-Ad	bronchial
25	chr2:160869000-160879200	Weak transcription	Aorta	Aorta
26	chr2:160869000-160879200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr2:160869000-160880800	Weak transcription	Gastric	stomach
28	chr2:160869200-160878000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr2:160869200-160878600	Weak transcription	Colon Smooth Muscle	Colon
30	chr2:160869200-160879000	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr2:160869400-160879200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr2:160871200-160878800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:160872200-160878600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:160872400-160881600	Strong transcription	Adipose Nuclei	Adipose
35	chr2:160875400-160879400	Strong transcription	HSMMtube	muscle
36	chr2:160875600-160879000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr2:160875600-160881600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:160876000-160878600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:160876200-160878200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr2:160876200-160879200	Weak transcription	Colonic Mucosa	Colon
41	chr2:160876600-160879000	Weak transcription	Duodenum Mucosa	Duodenum
42	chr2:160876800-160895800	Weak transcription	Stomach Smooth Muscle	stomach
43	chr2:160877200-160878000	Weak transcription	Fetal Intestine Large	intestine
44	chr2:160877200-160878600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:160877200-160878600	Weak transcription	Fetal Intestine Small	intestine
46	chr2:160877200-160881000	Weak transcription	Ovary	ovary
47	chr2:160877400-160879400	Strong transcription	HSMM	muscle

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