Variant report

Variant	rs9349684
Chromosome Location	chr6:53720196-53720197
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53719967..53722619-chr6:53723859..53726928,3	MCF-7	breast:
2	chr6:53720118..53721729-chr6:53744956..53746701,2	K562	blood:

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10948783	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10948784	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12193567	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12194768	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12209621	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3003498	0.80[JPT][hapmap]
rs3935664	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4128619	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4236114	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4260754	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4265034	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4273680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4331986	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4392712	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4486000	0.80[JPT][hapmap]
rs4515373	0.84[ASN][1000 genomes]
rs4582388	0.80[ASN][1000 genomes]
rs4583974	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4612163	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4624872	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4645423	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4715429	0.82[ASN][1000 genomes]
rs6458967	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6458968	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6904545	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6906921	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6907027	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6910777	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6913431	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6925391	0.82[ASN][1000 genomes]
rs6935621	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6935838	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7453639	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7745548	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7749635	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7749749	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7751036	1.00[CEU][hapmap];0.86[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7755924	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7761285	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9296722	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9296723	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9349682	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9349683	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9367543	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9370234	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9370237	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9370238	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9370240	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9382240	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9382242	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9382245	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9382247	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9395879	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9395880	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9395882	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9395883	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9395884	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9395887	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9463988	0.82[ASN][1000 genomes]
rs9463996	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs9463997	0.90[CHB][hapmap]

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:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53680400-53721600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:53695000-53743200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:53703200-53720200	Weak transcription	Aorta	Aorta
4	chr6:53703200-53726400	Weak transcription	Fetal Stomach	stomach
5	chr6:53703800-53727600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr6:53706000-53720200	Weak transcription	Esophagus	oesophagus
7	chr6:53706000-53722400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:53706200-53722000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr6:53706400-53720200	Weak transcription	Fetal Muscle Leg	muscle
10	chr6:53709800-53762200	Weak transcription	Primary B cells from cord blood	blood
11	chr6:53710400-53720400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr6:53711200-53720400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr6:53712600-53720400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr6:53712800-53721600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr6:53713000-53720200	Weak transcription	Dnd41	blood
16	chr6:53713000-53722000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr6:53716400-53720200	Weak transcription	Brain Angular Gyrus	brain
18	chr6:53717800-53731800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr6:53718400-53721200	Enhancers	Fetal Intestine Small	intestine
20	chr6:53718400-53723400	Enhancers	Stomach Mucosa	stomach
21	chr6:53718600-53720600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr6:53718600-53720600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr6:53718600-53721400	Enhancers	Duodenum Mucosa	Duodenum
24	chr6:53718800-53720600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:53718800-53720600	Enhancers	NHEK	skin
26	chr6:53718800-53721200	Enhancers	Fetal Intestine Large	intestine
27	chr6:53718800-53723400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:53719000-53720800	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr6:53719200-53720800	Enhancers	HMEC	breast
30	chr6:53719600-53720200	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr6:53719600-53720200	Enhancers	Colon Smooth Muscle	Colon
32	chr6:53719600-53720200	Enhancers	Gastric	stomach
33	chr6:53719600-53720600	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr6:53719600-53720600	Enhancers	Pancreas	Pancrea
35	chr6:53719800-53720400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:53719800-53720400	Enhancers	Fetal Thymus	thymus
37	chr6:53719800-53720400	Enhancers	Rectal Smooth Muscle	rectum
38	chr6:53719800-53720600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr6:53719800-53720600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:53719800-53720800	Enhancers	Small Intestine	intestine
41	chr6:53719800-53721600	Enhancers	Fetal Heart	heart
42	chr6:53719800-53722000	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr6:53719800-53727600	Enhancers	Brain Substantia Nigra	brain
44	chr6:53719800-53727800	Enhancers	Brain Hippocampus Middle	brain
45	chr6:53719800-53747800	Weak transcription	Primary T cells from cord blood	blood
46	chr6:53720000-53720400	Flanking Active TSS	HepG2	liver
47	chr6:53720000-53721000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr6:53720000-53721400	Enhancers	HSMMtube	muscle
49	chr6:53720000-53721800	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr6:53720000-53722600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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