Variant report

Variant	rs41289345
Chromosome Location	chr6:101306733-101306734
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	chr6:101299454..101302050-chr6:101304670..101307311,3	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12183204	0.86[ASN][1000 genomes]
rs1336240	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1336247	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1336248	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1336249	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1472299	0.86[ASN][1000 genomes]
rs1577618	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1889888	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2172843	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3736784	0.86[ASN][1000 genomes]
rs3736785	0.86[ASN][1000 genomes]
rs41288407	0.86[ASN][1000 genomes]
rs41288409	0.86[ASN][1000 genomes]
rs41288411	0.86[ASN][1000 genomes]
rs4839788	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4840143	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4840145	0.86[ASN][1000 genomes]
rs4840146	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4840149	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4840152	0.86[ASN][1000 genomes]
rs59852351	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62422696	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6902414	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6908453	0.86[ASN][1000 genomes]
rs6923187	0.82[EUR][1000 genomes]
rs6925086	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6932921	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6939613	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73506930	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7741877	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7751872	0.86[ASN][1000 genomes]
rs7756019	0.86[ASN][1000 genomes]
rs7757823	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7764514	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7770430	0.86[ASN][1000 genomes]
rs7773317	0.86[ASN][1000 genomes]
rs9322169	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9373587	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9377215	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9390683	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9399681	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9399691	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9404014	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9485416	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9485419	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9498396	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9498401	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9498405	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949535	chr6:100740293-101469052	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1020692	chr6:101136992-101426071	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv886457	chr6:101158950-101487473	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1020400	chr6:101172705-101981665	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv538390	chr6:101172705-101981665	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv1019213	chr6:101225650-101623140	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv538391	chr6:101225650-101623140	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	esv2763587	chr6:101277874-101510491	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:101215200-101311400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:101269200-101326600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:101275800-101314400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr6:101278000-101313800	Weak transcription	Fetal Intestine Small	intestine
5	chr6:101281200-101317000	Weak transcription	Small Intestine	intestine
6	chr6:101282000-101311400	Weak transcription	Aorta	Aorta
7	chr6:101285600-101326600	Weak transcription	NHLF	lung
8	chr6:101287800-101313000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr6:101290200-101318200	Weak transcription	Fetal Lung	lung
10	chr6:101290600-101312800	Weak transcription	Fetal Brain Male	brain
11	chr6:101290800-101311400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr6:101290800-101311600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:101291200-101326400	Weak transcription	Brain Anterior Caudate	brain
14	chr6:101291400-101314000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:101291600-101314000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr6:101291800-101312800	Weak transcription	Gastric	stomach
17	chr6:101292600-101310800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr6:101294000-101320400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr6:101294200-101314200	Weak transcription	Colon Smooth Muscle	Colon
20	chr6:101294600-101307000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr6:101294600-101310800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr6:101294600-101311400	Weak transcription	Pancreas	Pancrea
23	chr6:101294600-101314400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr6:101294600-101320600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr6:101294600-101325400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr6:101294600-101328600	Weak transcription	Spleen	Spleen
27	chr6:101294800-101325600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr6:101295000-101325800	Weak transcription	Brain Angular Gyrus	brain
29	chr6:101295000-101325800	Weak transcription	Stomach Smooth Muscle	stomach
30	chr6:101296000-101323400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr6:101296200-101306800	Weak transcription	HUVEC	blood vessel
32	chr6:101296600-101306800	Weak transcription	HepG2	liver
33	chr6:101296600-101310000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr6:101296800-101307200	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr6:101296800-101308400	Weak transcription	Adipose Nuclei	Adipose
36	chr6:101296800-101310200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr6:101296800-101317000	Weak transcription	HSMMtube	muscle
38	chr6:101296800-101323800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr6:101297000-101310800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr6:101297000-101310800	Weak transcription	Fetal Thymus	thymus
41	chr6:101297000-101311400	Weak transcription	Fetal Muscle Trunk	muscle
42	chr6:101297000-101311400	Weak transcription	Left Ventricle	heart
43	chr6:101297000-101327200	Weak transcription	Fetal Muscle Leg	muscle
44	chr6:101297000-101328200	Weak transcription	Ovary	ovary
45	chr6:101300200-101311400	Weak transcription	Thymus	Thymus
46	chr6:101300200-101319000	Weak transcription	Fetal Stomach	stomach
47	chr6:101300200-101326600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr6:101300200-101328400	Weak transcription	Esophagus	oesophagus
49	chr6:101300200-101328400	Weak transcription	Lung	lung
50	chr6:101300400-101311400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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