Variant report

Variant	rs17088269
Chromosome Location	chr6:150049261-150049262
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:150038960..150040762-chr6:150048383..150050938,2	MCF-7	breast:
2	chr6:150039916..150042698-chr6:150047893..150050444,2	MCF-7	breast:
3	chr6:150037459..150041467-chr6:150046998..150054266,14	K562	blood:
4	chr6:149967346..149970851-chr6:150047639..150051197,3	K562	blood:
5	chr6:150048960..150051066-chr6:150070232..150072342,2	K562	blood:
6	chr6:150043756..150046573-chr6:150046900..150049362,3	K562	blood:
7	chr6:150043754..150045572-chr6:150046900..150050197,3	K562	blood:

Variant related genes	Relation type
ENSG00000186625	Chromatin interaction
ENSG00000131023	Chromatin interaction
ENSG00000120265	Chromatin interaction
ENSG00000120253	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11961451	0.83[EUR][1000 genomes]
rs11961781	1.00[TSI][hapmap]
rs11963610	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11966407	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11968366	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11968879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs17078923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3806983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56149740	1.00[ASN][1000 genomes]
rs57880524	0.83[EUR][1000 genomes]
rs58651413	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6899595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6927395	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73606794	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7745198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7753340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9478983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9765961	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9766101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886762	chr6:149866452-150174507	Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv1792620	chr6:149909491-150083621	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	esv3475167	chr6:150003006-150086225	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	esv3475168	chr6:150003006-150086225	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	esv1803291	chr6:150018508-150164190	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150039600-150049600	Weak transcription	Spleen	Spleen
2	chr6:150039600-150049800	Weak transcription	Gastric	stomach
3	chr6:150039600-150050400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:150039800-150049800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:150039800-150049800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:150039800-150066800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:150039800-150067000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr6:150040000-150049400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:150040000-150049400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr6:150040000-150049600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:150040000-150049600	Weak transcription	Brain Substantia Nigra	brain
12	chr6:150040000-150049800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:150040000-150049800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr6:150040000-150049800	Weak transcription	Aorta	Aorta
15	chr6:150040000-150049800	Weak transcription	Brain Angular Gyrus	brain
16	chr6:150040000-150049800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr6:150040000-150049800	Weak transcription	Fetal Lung	lung
18	chr6:150040000-150049800	Weak transcription	Pancreas	Pancrea
19	chr6:150040000-150050000	Weak transcription	Esophagus	oesophagus
20	chr6:150040000-150050400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr6:150040000-150050400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr6:150040000-150050400	Weak transcription	Lung	lung
23	chr6:150040000-150051800	Weak transcription	Small Intestine	intestine
24	chr6:150040000-150056400	Weak transcription	Psoas Muscle	Psoas
25	chr6:150040000-150057400	Weak transcription	A549	lung
26	chr6:150040000-150066600	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr6:150040200-150049400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr6:150040200-150049400	Weak transcription	Brain Germinal Matrix	brain
29	chr6:150040200-150049600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr6:150040200-150049600	Weak transcription	Thymus	Thymus
31	chr6:150040200-150049600	Weak transcription	Hela-S3	cervix
32	chr6:150040200-150049800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr6:150040200-150056200	Weak transcription	Colonic Mucosa	Colon
34	chr6:150040400-150066200	Weak transcription	Fetal Brain Male	brain
35	chr6:150040600-150049600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr6:150043600-150065600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:150043600-150066000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:150043800-150049400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr6:150043800-150053800	Strong transcription	Dnd41	blood
40	chr6:150043800-150064000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr6:150044000-150065200	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr6:150044000-150065400	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr6:150044200-150058800	Strong transcription	Fetal Muscle Trunk	muscle
44	chr6:150044200-150065000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr6:150044200-150065200	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr6:150044600-150059200	Strong transcription	Fetal Muscle Leg	muscle
47	chr6:150044800-150065000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr6:150045200-150049600	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr6:150045400-150065600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr6:150045800-150065400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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