Variant report

Variant	rs7641825
Chromosome Location	chr3:105567658-105567659
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:105567530..105570429-chr3:105573055..105575422,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CD47-8	chr3:105565135-105569968	NONHSAT090970

Extended variants
information (count: 52 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10460808	0.91[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs10511246	0.86[ASW][hapmap];0.87[CEU][hapmap];0.82[LWK][hapmap];0.81[TSI][hapmap];0.80[YRI][hapmap];0.87[EUR][1000 genomes]
rs11921710	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11924742	0.93[CEU][hapmap]
rs12486371	0.84[ASW][hapmap]
rs1443108	0.85[ASW][hapmap]
rs16844736	0.91[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs1867189	0.85[ASW][hapmap]
rs1867192	0.93[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1910499	0.93[CEU][hapmap];0.81[TSI][hapmap]
rs1992521	0.86[ASN][1000 genomes]
rs2028597	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs2089091	0.86[ASW][hapmap];0.93[CEU][hapmap];0.83[LWK][hapmap];0.86[MKK][hapmap];0.81[TSI][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2197209	0.93[CEU][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2301036	0.84[ASN][1000 genomes]
rs2301043	0.85[ASW][hapmap]
rs2305035	0.85[ASW][hapmap]
rs2305036	0.85[ASW][hapmap]
rs3772515	0.85[ASW][hapmap]
rs3772540	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs3996189	0.81[CEU][hapmap]
rs4894957	0.81[CEU][hapmap]
rs57520912	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58340800	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6437620	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6437621	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6437624	0.81[CEU][hapmap]
rs6767627	0.93[CEU][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6788366	0.81[CEU][hapmap]
rs6807382	0.81[CEU][hapmap]
rs7619449	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7619647	0.85[ASW][hapmap]
rs7629357	0.93[CEU][hapmap];0.82[CHB][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7639888	0.92[ASW][hapmap];0.89[YRI][hapmap]
rs7648842	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7649466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7651784	0.81[CEU][hapmap]
rs9631436	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9657904	0.93[CEU][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs9820060	0.86[YRI][hapmap]
rs9826886	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9841500	0.81[CEU][hapmap]
rs9846534	0.93[CEU][hapmap];0.80[YRI][hapmap];0.89[EUR][1000 genomes]
rs9869648	0.93[CEU][hapmap]
rs9874600	0.93[CEU][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9876110	0.92[ASW][hapmap];0.94[YRI][hapmap]
rs9880744	0.94[YRI][hapmap]
rs9880861	0.85[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
2	nsv1008564	chr3:105554580-105643435	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1008876	chr3:105554580-105645373	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv877312	chr3:105560638-105916506	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers 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:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105533800-105570000	Weak transcription	Dnd41	blood
2	chr3:105540800-105569600	Weak transcription	Fetal Thymus	thymus
3	chr3:105543400-105581200	Weak transcription	Gastric	stomach
4	chr3:105543800-105571000	Weak transcription	Lung	lung
5	chr3:105544200-105584600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:105546600-105586200	Weak transcription	Esophagus	oesophagus
7	chr3:105549000-105571800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:105550000-105569600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr3:105555800-105576600	Weak transcription	Psoas Muscle	Psoas
10	chr3:105556200-105570200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:105556200-105571600	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr3:105556200-105579000	Weak transcription	Stomach Mucosa	stomach
13	chr3:105556400-105568000	Weak transcription	HSMM	muscle
14	chr3:105556600-105569600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr3:105556600-105569800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr3:105557800-105579200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr3:105557800-105586200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:105558200-105571800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:105558600-105586600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr3:105561600-105569600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr3:105561600-105569600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr3:105561600-105569600	Weak transcription	Fetal Muscle Leg	muscle
23	chr3:105561600-105586200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:105561800-105569800	Weak transcription	HSMMtube	muscle
25	chr3:105562000-105586000	Weak transcription	K562	blood
26	chr3:105562600-105568400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr3:105562600-105568800	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr3:105562600-105568800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr3:105562800-105568200	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr3:105563000-105569600	Weak transcription	Fetal Muscle Trunk	muscle
31	chr3:105563000-105584600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr3:105563000-105586800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:105563200-105567800	Weak transcription	NH-A	brain
34	chr3:105563200-105569400	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr3:105563200-105569600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr3:105563200-105569600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:105563200-105569600	Weak transcription	Liver	Liver
38	chr3:105563200-105569600	Weak transcription	Left Ventricle	heart
39	chr3:105563200-105571600	Weak transcription	Fetal Intestine Small	intestine
40	chr3:105563200-105572000	Weak transcription	HUVEC	blood vessel
41	chr3:105563200-105572200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr3:105563400-105569600	Weak transcription	Primary B cells from peripheral blood	blood
43	chr3:105563400-105570200	Weak transcription	Fetal Brain Female	brain
44	chr3:105563400-105583000	Weak transcription	Spleen	Spleen
45	chr3:105563600-105568400	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr3:105563600-105568800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr3:105563800-105584400	Weak transcription	Brain Angular Gyrus	brain
48	chr3:105564600-105569600	Weak transcription	Brain Cingulate Gyrus	brain
49	chr3:105564600-105569800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr3:105564800-105569600	Weak transcription	HepG2	liver

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