Variant report

Variant	rs1616375
Chromosome Location	chr6:106995863-106995864
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:106988236..106991971-chr6:106994585..106996382,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112297	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1111830	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1613722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs1676008	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1676010	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1676023	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1676024	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1676025	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1676026	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1676028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs17067603	1.00[JPT][hapmap]
rs17565194	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1770718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1770719	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1770720	1.00[CEU][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs1770721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1770722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1770723	1.00[ASN][1000 genomes]
rs1770733	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2066201	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2247335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2615209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3747789	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3804344	1.00[JPT][hapmap]
rs4946762	1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs6902745	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911321	1.00[JPT][hapmap]
rs72945076	0.89[ASN][1000 genomes]
rs7771502	0.96[ASN][1000 genomes]
rs783395	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs783396	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs783401	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs783414	1.00[CHB][hapmap]
rs9386565	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]

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	nsv932155	chr6:106281728-107030467	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532047	chr6:106591482-107143252	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv870375	chr6:106696090-107047892	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv1017419	chr6:106984669-106997000	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106961000-107001400	Weak transcription	Gastric	stomach
2	chr6:106964800-107029800	Weak transcription	Small Intestine	intestine
3	chr6:106970600-107022400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:106979000-107001400	Weak transcription	Pancreas	Pancrea
5	chr6:106982400-107000800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr6:106985800-107019200	Weak transcription	Aorta	Aorta
7	chr6:106988200-107001400	Weak transcription	Lung	lung
8	chr6:106991200-106999600	Strong transcription	Dnd41	blood
9	chr6:106992600-106996400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:106992600-106996600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:106993200-106996400	Genic enhancers	Primary B cells from peripheral blood	blood
12	chr6:106993200-106996600	Enhancers	Primary hematopoietic stem cells	blood
13	chr6:106993400-106996000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
14	chr6:106993400-106996000	Enhancers	Adipose Nuclei	Adipose
15	chr6:106993600-106996200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:106993600-106998400	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr6:106993800-106996200	Enhancers	HSMM	muscle
18	chr6:106993800-106996400	Enhancers	Fetal Lung	lung
19	chr6:106993800-106996400	Enhancers	Osteobl	bone
20	chr6:106993800-106996600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:106993800-106996600	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr6:106993800-106996600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:106993800-106996600	Enhancers	NH-A	brain
24	chr6:106994000-106996000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:106994000-106996000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr6:106994000-106996600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr6:106994000-106996600	Enhancers	HepG2	liver
28	chr6:106994000-107017800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr6:106994200-106996400	Enhancers	A549	lung
30	chr6:106994200-106997000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:106994200-107000200	Weak transcription	Esophagus	oesophagus
32	chr6:106994200-107009000	Weak transcription	Left Ventricle	heart
33	chr6:106994200-107019400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr6:106994200-107019600	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr6:106994400-106996600	Enhancers	Fetal Thymus	thymus
36	chr6:106994400-107000800	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr6:106994600-106996200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr6:106994600-106996200	Genic enhancers	Duodenum Mucosa	Duodenum
39	chr6:106994600-106996400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:106994600-106996400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:106994600-106996600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:106994600-106996600	Enhancers	Muscle Satellite Cultured Cells	--
43	chr6:106994600-106996600	Enhancers	Fetal Intestine Large	intestine
44	chr6:106994600-106996600	Enhancers	NHDF-Ad	bronchial
45	chr6:106994600-106997000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr6:106994600-106999600	Strong transcription	GM12878-XiMat	blood
47	chr6:106994600-107001400	Weak transcription	Spleen	Spleen
48	chr6:106994800-106996000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr6:106994800-106996600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr6:106994800-106996600	Enhancers	Fetal Intestine Small	intestine

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