Variant report

Variant	rs9349688
Chromosome Location	chr6:53762092-53762093
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:53656897..53659493-chr6:53761519..53764190,2	MCF-7	breast:
2	chr6:53762030..53763793-chr6:53766610..53769238,2	K562	blood:
3	chr6:53658003..53661246-chr6:53761452..53764379,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137269	Chromatin interaction
ENSG00000228614	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs3813848	1.00[ASW][hapmap]
rs55906536	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9296724	1.00[AFR][1000 genomes]
rs9349687	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9357772	0.81[CHB][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap]
rs9370243	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9395885	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9463990	1.00[AFR][1000 genomes]
rs9463995	1.00[AFR][1000 genomes]
rs9463999	1.00[AFR][1000 genomes]
rs9474685	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv830664	chr6:53698021-53825270	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53709800-53762200	Weak transcription	Primary B cells from cord blood	blood
2	chr6:53737800-53768400	Weak transcription	Esophagus	oesophagus
3	chr6:53739000-53767800	Weak transcription	Ovary	ovary
4	chr6:53739000-53771800	Weak transcription	Pancreas	Pancrea
5	chr6:53742200-53766200	Weak transcription	Fetal Stomach	stomach
6	chr6:53744000-53762400	Weak transcription	Placenta	Placenta
7	chr6:53744600-53764200	Weak transcription	Fetal Intestine Small	intestine
8	chr6:53745600-53762200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr6:53746800-53768400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr6:53747600-53767800	Weak transcription	Small Intestine	intestine
11	chr6:53749200-53763600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr6:53749200-53765800	Weak transcription	Primary T cells from cord blood	blood
13	chr6:53749400-53762600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr6:53752400-53771000	Weak transcription	Gastric	stomach
15	chr6:53752400-53771800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:53752800-53782000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr6:53754800-53775600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr6:53754800-53779800	Weak transcription	NHLF	lung
19	chr6:53755000-53779800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr6:53756000-53781800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr6:53757800-53767400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr6:53757800-53768000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr6:53758000-53775600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:53759200-53762400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr6:53759200-53762400	Weak transcription	Left Ventricle	heart
26	chr6:53759200-53767600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr6:53759200-53767600	Weak transcription	Lung	lung
28	chr6:53759200-53767800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr6:53759200-53769400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr6:53759200-53770800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr6:53759200-53787600	Weak transcription	Spleen	Spleen
32	chr6:53759200-53794400	Weak transcription	Right Ventricle	heart
33	chr6:53759400-53762200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:53759400-53767600	Weak transcription	Thymus	Thymus
35	chr6:53759400-53768200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr6:53759400-53770000	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr6:53759400-53771800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr6:53759400-53786400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr6:53759600-53767000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr6:53759600-53789800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr6:53760400-53789400	Weak transcription	Stomach Mucosa	stomach
42	chr6:53760400-53791200	Weak transcription	Hela-S3	cervix
43	chr6:53760600-53773000	Strong transcription	Dnd41	blood
44	chr6:53760600-53778800	Weak transcription	Fetal Muscle Leg	muscle
45	chr6:53760600-53793600	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr6:53760800-53762200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:53760800-53762400	Weak transcription	Brain Hippocampus Middle	brain
48	chr6:53760800-53763000	Weak transcription	Fetal Brain Female	brain
49	chr6:53760800-53771800	Weak transcription	Brain Angular Gyrus	brain
50	chr6:53761000-53762200	Weak transcription	HepG2	liver

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