Variant report

Variant	rs6543088
Chromosome Location	chr2:98372281-98372282
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:98367186..98369342-chr2:98372074..98374129,2	MCF-7	breast:
2	chr2:98371656..98373515-chr2:98376477..98379656,3	MCF-7	breast:
3	chr2:98370843..98373809-chr2:98614245..98616130,2	K562	blood:
4	chr2:98367567..98369745-chr2:98371169..98373784,2	K562	blood:
5	chr2:98372004..98373640-chr2:98374826..98376780,2	MCF-7	breast:
6	chr2:98371016..98372901-chr2:98373770..98376457,3	K562	blood:

Variant related genes	Relation type
ENSG00000075568	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10166513	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10167772	0.85[ASN][1000 genomes]
rs10168543	0.91[ASN][1000 genomes]
rs10175129	0.85[ASN][1000 genomes]
rs10180434	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[JPT][hapmap];0.81[MKK][hapmap];0.85[ASN][1000 genomes]
rs10180722	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10183768	0.85[ASN][1000 genomes]
rs10187061	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10188497	0.91[ASN][1000 genomes]
rs10188713	1.00[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.81[MKK][hapmap];0.91[ASN][1000 genomes]
rs10189414	0.85[ASN][1000 genomes]
rs10191101	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10191483	0.82[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes]
rs10192322	0.82[CHB][hapmap]
rs10202138	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10206684	0.85[ASN][1000 genomes]
rs10210520	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11893437	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs11894541	0.85[ASN][1000 genomes]
rs11894895	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11897301	0.91[ASN][1000 genomes]
rs12712117	0.91[ASN][1000 genomes]
rs12712120	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12712172	0.85[ASN][1000 genomes]
rs12992955	0.85[ASN][1000 genomes]
rs13000585	0.85[ASN][1000 genomes]
rs13004862	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13008904	0.85[ASN][1000 genomes]
rs13009300	0.82[AMR][1000 genomes]
rs13010004	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1446327	0.91[ASN][1000 genomes]
rs17489259	0.83[AMR][1000 genomes]
rs1960329	1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs1982336	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs2121271	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2293679	0.85[CHB][hapmap]
rs34190123	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34305873	1.00[ASN][1000 genomes]
rs34414288	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34635139	0.82[AMR][1000 genomes]
rs35185431	0.91[ASN][1000 genomes]
rs35203092	0.91[ASN][1000 genomes]
rs35263587	0.80[AMR][1000 genomes]
rs35776557	0.82[ASN][1000 genomes]
rs35807655	0.85[ASN][1000 genomes]
rs3821053	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs55753459	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6543111	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6707719	0.85[CHB][hapmap]
rs6712078	1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs6721323	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs6728312	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6738401	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6751727	0.85[ASN][1000 genomes]
rs6755021	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6760008	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6875	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];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71429373	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs718159	0.91[ASN][1000 genomes]
rs7557495	0.85[ASN][1000 genomes]
rs7570009	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7582298	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7593290	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7594928	0.85[ASN][1000 genomes]
rs7595039	0.91[ASN][1000 genomes]
rs7599043	0.85[ASN][1000 genomes]
rs9808558	0.85[CHB][hapmap]
rs9973490	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][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	nsv531382	chr2:98250628-98457616	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98348200-98372400	Weak transcription	Esophagus	oesophagus
2	chr2:98352200-98398800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:98355000-98373200	Weak transcription	Gastric	stomach
4	chr2:98359200-98382400	Weak transcription	Psoas Muscle	Psoas
5	chr2:98361000-98373200	Weak transcription	Ovary	ovary
6	chr2:98363200-98375600	Weak transcription	Hela-S3	cervix
7	chr2:98363800-98373200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr2:98364200-98373400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:98364600-98374800	Weak transcription	Stomach Mucosa	stomach
10	chr2:98364600-98375000	Weak transcription	Fetal Brain Male	brain
11	chr2:98365000-98373200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:98365400-98372400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr2:98365400-98372400	Weak transcription	K562	blood
14	chr2:98365400-98373400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:98365400-98375000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr2:98365400-98375400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr2:98365400-98375800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr2:98366000-98374200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr2:98366200-98400000	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr2:98366400-98376800	Strong transcription	Duodenum Mucosa	Duodenum
21	chr2:98366400-98384600	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr2:98366800-98377600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr2:98367200-98385000	Strong transcription	Primary B cells from peripheral blood	blood
24	chr2:98367400-98380000	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr2:98368000-98393800	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr2:98368400-98377000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr2:98368400-98383600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr2:98368600-98373600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr2:98368600-98413000	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr2:98368800-98373200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:98369200-98373400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr2:98369200-98381200	Weak transcription	Fetal Heart	heart
33	chr2:98369400-98372400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr2:98369400-98376600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:98369600-98398800	Strong transcription	Fetal Muscle Leg	muscle
36	chr2:98369800-98373200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr2:98369800-98373600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr2:98369800-98374800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr2:98369800-98384800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr2:98370000-98372400	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr2:98370200-98376800	Weak transcription	NHDF-Ad	bronchial
42	chr2:98370200-98392600	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr2:98370400-98376600	Strong transcription	Primary T cells from cord blood	blood
44	chr2:98370400-98382800	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr2:98370400-98383600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:98370400-98386400	Strong transcription	Fetal Intestine Small	intestine
47	chr2:98370600-98381800	Strong transcription	Lung	lung
48	chr2:98370600-98384400	Strong transcription	Fetal Muscle Trunk	muscle
49	chr2:98370600-98384400	Strong transcription	Placenta	Placenta
50	chr2:98370600-98392400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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