Variant report

Variant	rs10949295
Chromosome Location	chr6:15356641-15356642
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:15356510..15359916-chr6:15362277..15365579,4	MCF-7	breast:
2	chr6:15354841..15359514-chr6:15360955..15363291,4	MCF-7	breast:

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10484355	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs10949292	0.83[EUR][1000 genomes]
rs10949294	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11756544	1.00[JPT][hapmap]
rs11757415	1.00[JPT][hapmap]
rs11759478	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes]
rs11759828	0.85[AMR][1000 genomes]
rs12192599	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes]
rs12198692	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs12198694	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12199895	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12201889	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12204124	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs12205420	0.85[AMR][1000 genomes]
rs12206745	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs12209228	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12209453	0.85[AMR][1000 genomes]
rs12209748	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12210592	1.00[CEU][hapmap]
rs12211278	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211777	0.91[EUR][1000 genomes]
rs12212013	0.85[AMR][1000 genomes]
rs12214719	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12215596	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs12215740	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13192347	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs13194410	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13195950	1.00[JPT][hapmap]
rs13205396	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs13205612	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs13208486	1.00[JPT][hapmap]
rs13214720	0.97[ASN][1000 genomes]
rs16876250	0.91[EUR][1000 genomes]
rs16876278	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16876354	1.00[JPT][hapmap]
rs17575737	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17576233	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17576436	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17576710	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17619730	0.82[CEU][hapmap]
rs17619838	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17637773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17638192	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17638720	1.00[JPT][hapmap]
rs17687211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17713010	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs2237146	1.00[JPT][hapmap]
rs2299051	1.00[JPT][hapmap]
rs2299057	0.83[ASN][1000 genomes]
rs28505073	0.83[AMR][1000 genomes]
rs35139070	0.83[ASN][1000 genomes]
rs35629999	0.83[ASN][1000 genomes]
rs35734069	0.83[ASN][1000 genomes]
rs55634912	0.85[AMR][1000 genomes]
rs56265026	1.00[ASN][1000 genomes]
rs66478504	0.83[ASN][1000 genomes]
rs6919296	1.00[CHB][hapmap]
rs6935879	0.91[EUR][1000 genomes]
rs6938919	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs72834551	0.85[AMR][1000 genomes]
rs72834590	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs742102	1.00[JPT][hapmap]
rs7747437	1.00[JPT][hapmap]
rs7765425	1.00[CHB][hapmap]
rs7767966	1.00[JPT][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	nsv1027010	chr6:15201803-15425629	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1030558	chr6:15234675-15449137	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv538141	chr6:15234675-15509163	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv538142	chr6:15243960-15404893	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv949448	chr6:15279490-15449441	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1025512	chr6:15291551-15452395	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv538143	chr6:15291551-15452395	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv538144	chr6:15310696-15364984	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1019927	chr6:15351240-15419257	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv538145	chr6:15351240-15419257	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15327800-15375800	Weak transcription	Aorta	Aorta
2	chr6:15332000-15359400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:15341000-15362800	Weak transcription	Fetal Intestine Small	intestine
4	chr6:15341200-15359400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:15341400-15365400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr6:15341800-15362800	Weak transcription	Gastric	stomach
7	chr6:15341800-15378400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr6:15342800-15364600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr6:15345600-15357400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr6:15348800-15359000	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr6:15348800-15360000	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr6:15349200-15359000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr6:15349600-15360000	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr6:15349800-15358400	Genic enhancers	HUES48 Cell Line	embryonic stem cell
15	chr6:15350600-15357800	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr6:15351200-15358200	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr6:15351800-15358200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr6:15351800-15359200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr6:15352000-15363200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr6:15352000-15364400	Weak transcription	Esophagus	oesophagus
21	chr6:15352000-15370000	Weak transcription	Lung	lung
22	chr6:15352800-15358800	Weak transcription	HSMMtube	muscle
23	chr6:15352800-15359200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr6:15352800-15365600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr6:15353000-15359000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr6:15353200-15357000	Weak transcription	Fetal Muscle Leg	muscle
27	chr6:15353200-15357000	Weak transcription	Ovary	ovary
28	chr6:15353200-15357200	Weak transcription	Adipose Nuclei	Adipose
29	chr6:15353200-15357400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr6:15353200-15357600	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr6:15353200-15358000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr6:15353200-15362200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr6:15353200-15365400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:15353400-15357200	Weak transcription	Brain Anterior Caudate	brain
35	chr6:15353400-15357200	Weak transcription	Brain Substantia Nigra	brain
36	chr6:15353400-15362600	Weak transcription	A549	lung
37	chr6:15353400-15363600	Weak transcription	Thymus	Thymus
38	chr6:15353400-15364400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr6:15353400-15365400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr6:15353600-15357400	Weak transcription	Fetal Kidney	kidney
41	chr6:15353600-15359000	Weak transcription	NH-A	brain
42	chr6:15353600-15359200	Weak transcription	Colon Smooth Muscle	Colon
43	chr6:15353600-15365400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr6:15353800-15362600	Weak transcription	Stomach Mucosa	stomach
45	chr6:15353800-15365400	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr6:15354000-15357600	Genic enhancers	HUES6 Cell Line	embryonic stem cell
47	chr6:15354600-15356800	Genic enhancers	HUES64 Cell Line	embryonic stem cell
48	chr6:15354600-15359000	Weak transcription	HepG2	liver
49	chr6:15354600-15360800	Weak transcription	NHEK	skin
50	chr6:15354600-15364400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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