Variant report

Variant	rs13204935
Chromosome Location	chr6:1840779-1840780
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:1612577..1614591-chr6:1838798..1840944,2	MCF-7	breast:
2	chr6:1839714..1842732-chr6:1843630..1846250,4	MCF-7	breast:
3	chr6:1831250..1835471-chr6:1835503..1841068,8	MCF-7	breast:
4	chr6:1839588..1841532-chr6:1851475..1853574,2	MCF-7	breast:
5	chr6:1839372..1842046-chr6:1850595..1852706,2	MCF-7	breast:
6	chr6:1778842..1781326-chr6:1839801..1842724,2	MCF-7	breast:
7	chr6:1608467..1612521-chr6:1837362..1840946,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000054598	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs13190775	0.83[EUR][1000 genomes]
rs13197177	0.86[CHB][hapmap];0.83[EUR][1000 genomes]
rs1998519	0.80[EUR][1000 genomes]
rs35946812	0.83[EUR][1000 genomes]
rs3778536	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3778554	0.86[CHB][hapmap]
rs3800086	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs3800090	1.00[CEU][hapmap];0.86[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];0.86[ASN][1000 genomes]
rs3800105	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3823276	1.00[YRI][hapmap]
rs57347378	0.83[EUR][1000 genomes]
rs6596858	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6912444	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7764600	0.86[CHB][hapmap]
rs9501779	1.00[YRI][hapmap]
rs9503028	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9503031	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9503036	1.00[YRI][hapmap]
rs9503043	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv491607	chr6:1580681-1951526	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1020603	chr6:1697548-1921374	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv538093	chr6:1697548-1921374	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv869043	chr6:1744238-2006788	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv538094	chr6:1757776-1907505	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv931941	chr6:1768439-2246781	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
9	nsv883383	chr6:1775436-1918572	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv883384	chr6:1787862-1942538	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv1019895	chr6:1832936-1882435	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1829800-1856600	Weak transcription	Primary T cells from cord blood	blood
2	chr6:1833400-1843800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr6:1833400-1845800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr6:1833400-1856600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:1833600-1842000	Weak transcription	Left Ventricle	heart
6	chr6:1833600-1842000	Weak transcription	Right Atrium	heart
7	chr6:1833600-1842400	Weak transcription	Gastric	stomach
8	chr6:1833600-1843000	Weak transcription	Fetal Intestine Small	intestine
9	chr6:1833600-1845800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr6:1833600-1846000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:1833600-1849600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr6:1833800-1842000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr6:1834000-1848000	Weak transcription	HepG2	liver
14	chr6:1835600-1845800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr6:1838200-1862200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:1838400-1843200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:1838400-1845000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr6:1838400-1845800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr6:1838800-1846000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:1839200-1841600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:1839400-1840800	Enhancers	Aorta	Aorta
22	chr6:1839600-1844200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:1839800-1841400	Weak transcription	Fetal Kidney	kidney
24	chr6:1840000-1841200	Enhancers	Pancreas	Pancrea
25	chr6:1840400-1840800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:1840400-1841000	Enhancers	Osteobl	bone
27	chr6:1840400-1841200	Enhancers	Ovary	ovary
28	chr6:1840600-1840800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:1840600-1841200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:1840600-1841200	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr6:1840600-1841400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr6:1840600-1842000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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