Variant report

Variant	rs12205182
Chromosome Location	chr6:1839079-1839080
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:1612565..1615275-chr6:1837590..1839107,2	MCF-7	breast:
2	chr6:1838007..1840315-chr6:1844075..1845612,2	MCF-7	breast:
3	chr6:1613523..1614289-chr6:1838606..1839498,2	MCF-7	breast:
4	chr6:1612577..1614591-chr6:1838798..1840944,2	MCF-7	breast:
5	chr6:1641242..1642170-chr6:1838518..1839870,7	MCF-7	breast:
6	chr6:1831250..1835471-chr6:1835503..1841068,8	MCF-7	breast:
7	chr6:1762522..1764369-chr6:1837443..1839225,2	MCF-7	breast:
8	chr6:1608467..1612521-chr6:1837362..1840946,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000054598	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12209238	1.00[CEU][hapmap]
rs12213232	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72841949	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9391940	1.00[CEU][hapmap]
rs9405520	0.85[EUR][1000 genomes]

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:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1829800-1856600	Weak transcription	Primary T cells from cord blood	blood
2	chr6:1833000-1840000	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr6:1833400-1843800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr6:1833400-1845800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr6:1833400-1856600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:1833600-1839400	Weak transcription	Aorta	Aorta
7	chr6:1833600-1839400	Weak transcription	Stomach Mucosa	stomach
8	chr6:1833600-1840000	Weak transcription	Pancreas	Pancrea
9	chr6:1833600-1840400	Weak transcription	Osteobl	bone
10	chr6:1833600-1842000	Weak transcription	Left Ventricle	heart
11	chr6:1833600-1842000	Weak transcription	Right Atrium	heart
12	chr6:1833600-1842400	Weak transcription	Gastric	stomach
13	chr6:1833600-1843000	Weak transcription	Fetal Intestine Small	intestine
14	chr6:1833600-1845800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr6:1833600-1846000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr6:1833600-1849600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr6:1833800-1839200	Weak transcription	Liver	Liver
18	chr6:1833800-1842000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr6:1834000-1848000	Weak transcription	HepG2	liver
20	chr6:1835600-1845800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr6:1836600-1839400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:1836600-1839800	Enhancers	Fetal Kidney	kidney
23	chr6:1837200-1839400	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr6:1837600-1839200	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr6:1837600-1839400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:1837600-1839400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr6:1837600-1839600	Enhancers	Brain Germinal Matrix	brain
28	chr6:1837600-1840000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr6:1837600-1840000	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr6:1837600-1840000	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr6:1837800-1839200	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr6:1837800-1839200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:1837800-1839200	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr6:1837800-1839200	Enhancers	HMEC	breast
35	chr6:1837800-1839400	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr6:1837800-1839400	Enhancers	HUVEC	blood vessel
37	chr6:1837800-1839600	Enhancers	NHEK	skin
38	chr6:1838000-1839200	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr6:1838000-1839400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr6:1838000-1839600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
41	chr6:1838000-1839600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:1838000-1839600	Enhancers	NH-A	brain
43	chr6:1838000-1840000	Enhancers	Hela-S3	cervix
44	chr6:1838200-1840400	Weak transcription	Ovary	ovary
45	chr6:1838200-1862200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr6:1838400-1839400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:1838400-1839800	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr6:1838400-1840000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr6:1838400-1840200	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr6:1838400-1843200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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