Variant report

Variant	rs7641630
Chromosome Location	chr3:100124112-100124113
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:100116341..100122043-chr3:100122556..100129449,8	MCF-7	breast:
2	chr3:100102691..100105563-chr3:100122980..100125104,2	MCF-7	breast:
3	chr3:100117960..100119967-chr3:100122961..100124652,2	K562	blood:

Variant related genes	Relation type
ENSG00000206535	Chromatin interaction
ENSG00000154174	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10936180	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];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1123578	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1214380	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1214381	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1228184	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12495001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1530283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs166747	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs277620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs277622	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs277623	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs277626	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs277628	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs277629	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs277630	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs277633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs277634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs277635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs277638	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277639	0.82[MEX][hapmap]
rs277641	0.82[MEX][hapmap]
rs277642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs277644	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs277651	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs372438	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3772692	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3806615	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs392066	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes]
rs402870	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs413425	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs431069	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs432715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6780662	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6791102	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6794955	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[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];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7616634	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];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[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	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100119200-100124600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:100121000-100127000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:100121000-100127000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:100121000-100127000	Weak transcription	Gastric	stomach
5	chr3:100121400-100124200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr3:100121800-100131000	Weak transcription	Psoas Muscle	Psoas
7	chr3:100122000-100124400	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr3:100122000-100127000	Weak transcription	Aorta	Aorta
9	chr3:100122000-100143800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:100122400-100127000	Weak transcription	Thymus	Thymus
11	chr3:100122400-100132400	Weak transcription	Primary T cells from cord blood	blood
12	chr3:100122600-100124400	Weak transcription	Fetal Intestine Large	intestine
13	chr3:100122600-100126200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr3:100122600-100127000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:100122600-100127000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:100122600-100129800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:100122600-100132400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:100122600-100133600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:100122600-100149200	Weak transcription	Left Ventricle	heart
20	chr3:100122800-100126000	Weak transcription	Brain Hippocampus Middle	brain
21	chr3:100122800-100126000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr3:100122800-100126200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr3:100122800-100126400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:100122800-100127000	Weak transcription	Pancreas	Pancrea
25	chr3:100122800-100129800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:100122800-100131600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr3:100123000-100124200	Enhancers	Hela-S3	cervix
28	chr3:100123000-100129000	Weak transcription	NHLF	lung
29	chr3:100123000-100131600	Weak transcription	Fetal Heart	heart
30	chr3:100123000-100131600	Weak transcription	HSMM	muscle
31	chr3:100123000-100131800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:100123000-100132600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr3:100123000-100133600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr3:100123200-100124400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:100123200-100126000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr3:100123200-100126000	Weak transcription	Fetal Lung	lung
37	chr3:100123200-100127000	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr3:100123200-100127000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:100123200-100127000	Weak transcription	Ovary	ovary
40	chr3:100123200-100130200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:100123200-100133600	Weak transcription	A549	lung
42	chr3:100123200-100135400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:100123400-100124200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:100123400-100124400	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr3:100123400-100124400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr3:100123400-100124600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:100123400-100126000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:100123400-100127000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr3:100123400-100127000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:100123400-100130200	Weak transcription	K562	blood

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