Variant report

Variant	rs5742962
Chromosome Location	chr2:190653258-190653259
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:190647276..190650554-chr2:190651285..190655596,9	MCF-7	breast:
2	chr2:190651111..190653686-chr2:190669212..190673503,3	K562	blood:
3	chr2:190652358..190654600-chr2:190658326..190660113,2	K562	blood:
4	chr2:190649682..190653858-chr2:190657943..190661151,4	K562	blood:
5	chr2:190626395..190628968-chr2:190652066..190655379,3	K562	blood:

Variant related genes	Relation type
ENSG00000064933	Chromatin interaction
ENSG00000253559	Chromatin interaction
ENSG00000128694	Chromatin interaction
ENSG00000128699	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1046196	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233267	0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233270	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233273	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233274	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233286	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13404927	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs16831960	0.87[ASW][hapmap];0.86[LWK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs2544054	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs256571	1.00[JPT][hapmap]
rs5742924	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5742949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5742955	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5742965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5742976	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5742991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5742993	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5742994	0.81[EUR][1000 genomes]
rs5742997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5743003	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5743048	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5743067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5743090	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5743102	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5743130	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs5743161	1.00[CEU][hapmap]
rs5743164	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs5743169	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs5743175	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs58147864	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60386871	0.82[EUR][1000 genomes]
rs6750293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73042330	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73054335	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73054336	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73054339	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73054342	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs735558	0.82[EUR][1000 genomes]
rs7579156	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875616	chr2:190650460-190656614	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190649600-190656200	Weak transcription	Spleen	Spleen
2	chr2:190649600-190658600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:190649800-190657600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:190649800-190658600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:190649800-190662200	Weak transcription	Aorta	Aorta
6	chr2:190649800-190662200	Weak transcription	Left Ventricle	heart
7	chr2:190649800-190662800	Weak transcription	Lung	lung
8	chr2:190649800-190667200	Weak transcription	Pancreas	Pancrea
9	chr2:190649800-190675200	Weak transcription	Esophagus	oesophagus
10	chr2:190649800-190713400	Weak transcription	Gastric	stomach
11	chr2:190650000-190656000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr2:190650000-190657000	Weak transcription	Placenta	Placenta
13	chr2:190650000-190688200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:190650200-190656400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:190650200-190656800	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr2:190650200-190657600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr2:190650200-190658600	Weak transcription	Ovary	ovary
18	chr2:190650200-190662800	Weak transcription	Psoas Muscle	Psoas
19	chr2:190650200-190668200	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr2:190650200-190669200	Weak transcription	Right Ventricle	heart
21	chr2:190650200-190673000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:190650200-190673200	Weak transcription	Small Intestine	intestine
23	chr2:190650400-190653400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:190650400-190656200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr2:190650400-190656400	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr2:190650400-190656400	Weak transcription	Primary B cells from peripheral blood	blood
27	chr2:190650400-190656400	Weak transcription	Brain Anterior Caudate	brain
28	chr2:190650400-190656400	Weak transcription	Fetal Intestine Large	intestine
29	chr2:190650400-190657000	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr2:190650400-190657600	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr2:190650400-190657600	Weak transcription	Primary T cells from cord blood	blood
32	chr2:190650400-190657600	Weak transcription	Brain Angular Gyrus	brain
33	chr2:190650400-190657600	Weak transcription	Fetal Intestine Small	intestine
34	chr2:190650400-190659600	Weak transcription	HSMMtube	muscle
35	chr2:190650400-190662200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr2:190650400-190662200	Weak transcription	Brain Substantia Nigra	brain
37	chr2:190650400-190662600	Weak transcription	Brain Hippocampus Middle	brain
38	chr2:190650400-190662800	Weak transcription	Colon Smooth Muscle	Colon
39	chr2:190650400-190664600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr2:190650400-190666800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr2:190650400-190667400	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr2:190650400-190670400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr2:190650400-190675800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr2:190650400-190686800	Weak transcription	Thymus	Thymus
45	chr2:190650400-190688400	Weak transcription	Colonic Mucosa	Colon
46	chr2:190650400-190689800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr2:190650400-190711400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr2:190650600-190653400	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr2:190650600-190654000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr2:190650600-190656200	Weak transcription	Primary T helper cells PMA-I stimulated	--

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