Variant report

Variant	rs7639888
Chromosome Location	chr3:105545445-105545446
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:105539575..105542989-chr3:105543009..105546955,3	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1042852	0.84[ASW][hapmap]
rs11919893	0.83[CEU][hapmap]
rs12486371	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12487841	0.85[AMR][1000 genomes]
rs12496588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12497428	0.83[CEU][hapmap]
rs12632980	0.83[CEU][hapmap]
rs13090949	0.83[CEU][hapmap]
rs13317635	0.84[ASW][hapmap]
rs13433776	0.83[CEU][hapmap]
rs1443108	0.92[ASW][hapmap]
rs16851443	0.91[CHD][hapmap]
rs16851492	0.82[CHD][hapmap]
rs1867189	0.92[ASW][hapmap]
rs2089092	0.87[ASN][1000 genomes]
rs2301043	0.92[ASW][hapmap]
rs2305035	0.92[ASW][hapmap]
rs2305036	0.92[ASW][hapmap]
rs3772512	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3772515	0.92[ASW][hapmap]
rs56344829	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60536875	0.81[ASN][1000 genomes]
rs6437616	0.88[CEU][hapmap]
rs6437623	0.90[CEU][hapmap];0.91[AMR][1000 genomes]
rs6778745	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6780432	0.83[CEU][hapmap]
rs6791765	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6796362	0.80[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes]
rs72997629	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72997684	0.80[AMR][1000 genomes]
rs7619647	0.92[ASW][hapmap]
rs7624530	0.84[ASW][hapmap]
rs7634195	0.83[CEU][hapmap]
rs7638504	0.83[CEU][hapmap]
rs7641825	0.92[ASW][hapmap];0.89[YRI][hapmap]
rs7649466	0.89[YRI][hapmap]
rs7650147	0.81[CEU][hapmap];0.91[AMR][1000 genomes]
rs894541	0.83[CEU][hapmap]
rs9657910	1.00[TSI][hapmap]
rs9811776	0.83[CEU][hapmap]
rs9814582	0.83[CEU][hapmap]
rs9820060	0.89[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9838755	0.83[CEU][hapmap]
rs9841798	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs9872895	0.81[CEU][hapmap]
rs9876110	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];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9880744	1.00[CEU][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9880861	0.92[ASW][hapmap]

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	esv2755185	chr3:105378310-105597310	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105483200-105555200	Weak transcription	Placenta	Placenta
2	chr3:105505000-105548200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:105511400-105566400	Weak transcription	Aorta	Aorta
4	chr3:105521200-105546800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:105528400-105553600	Weak transcription	Fetal Kidney	kidney
6	chr3:105529000-105546600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr3:105531400-105546600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr3:105531600-105546400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:105532200-105563000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:105533600-105560600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr3:105533800-105570000	Weak transcription	Dnd41	blood
12	chr3:105534200-105566200	Weak transcription	Brain Germinal Matrix	brain
13	chr3:105534400-105546600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:105535600-105553800	Weak transcription	Fetal Brain Male	brain
15	chr3:105537800-105546800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr3:105539200-105546200	Weak transcription	Esophagus	oesophagus
17	chr3:105539400-105551600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:105540800-105569600	Weak transcription	Fetal Thymus	thymus
19	chr3:105541000-105554400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:105541400-105548000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr3:105541800-105553600	Weak transcription	Fetal Brain Female	brain
22	chr3:105542200-105546400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr3:105542200-105553600	Weak transcription	Liver	Liver
24	chr3:105542200-105554000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:105542400-105548200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:105542600-105546200	Weak transcription	GM12878-XiMat	blood
27	chr3:105542600-105548200	Weak transcription	Pancreas	Pancrea
28	chr3:105542600-105555400	Weak transcription	Brain Angular Gyrus	brain
29	chr3:105542600-105566000	Weak transcription	Fetal Stomach	stomach
30	chr3:105542800-105545600	Strong transcription	Primary B cells from cord blood	blood
31	chr3:105542800-105546400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:105542800-105546800	Weak transcription	Brain Hippocampus Middle	brain
33	chr3:105542800-105554400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr3:105543000-105546400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr3:105543000-105546800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:105543000-105555600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:105543200-105546000	Weak transcription	Adipose Nuclei	Adipose
38	chr3:105543200-105546200	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr3:105543200-105546400	Weak transcription	Right Atrium	heart
40	chr3:105543200-105546400	Weak transcription	HUVEC	blood vessel
41	chr3:105543200-105546600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr3:105543200-105546600	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr3:105543200-105548400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:105543200-105550200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:105543200-105551600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr3:105543400-105546000	Weak transcription	A549	lung
47	chr3:105543400-105546200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr3:105543400-105546200	Weak transcription	K562	blood
49	chr3:105543400-105546400	Weak transcription	Ovary	ovary
50	chr3:105543400-105546800	Weak transcription	Psoas Muscle	Psoas

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