Variant report

Variant	rs4128619
Chromosome Location	chr6:53710249-53710250
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10948783	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10948784	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12193567	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12194768	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12209621	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3935664	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4236114	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4260754	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4265034	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4273680	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4331986	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4392712	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4583974	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4612163	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4624872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4645423	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6458967	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6458968	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6904545	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6906921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6907027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6910777	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6913431	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6935621	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6935838	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7453639	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7745548	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7749635	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7749749	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7751036	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7755924	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7761285	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9296722	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9296723	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9349682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9349683	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9349684	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9367543	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9370234	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9370237	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9370238	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9370240	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9382240	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9382242	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9382243	0.86[CHB][hapmap]
rs9382244	0.80[ASN][1000 genomes]
rs9382245	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9382247	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9382254	0.85[CHB][hapmap]
rs9395879	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9395880	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9395881	0.80[ASN][1000 genomes]
rs9395882	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9395883	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9395884	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9395887	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][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:51 , 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	chr6:53693400-53720000	Weak transcription	Left Ventricle	heart
3	chr6:53695000-53719800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:53695000-53743200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:53697200-53718600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr6:53698000-53715600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr6:53703000-53718600	Weak transcription	Pancreas	Pancrea
8	chr6:53703200-53710400	Weak transcription	HUVEC	blood vessel
9	chr6:53703200-53720000	Weak transcription	HSMMtube	muscle
10	chr6:53703200-53720200	Weak transcription	Aorta	Aorta
11	chr6:53703200-53726400	Weak transcription	Fetal Stomach	stomach
12	chr6:53703600-53710600	Weak transcription	Brain Hippocampus Middle	brain
13	chr6:53703800-53717200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr6:53703800-53727600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr6:53704400-53710600	Weak transcription	Colon Smooth Muscle	Colon
16	chr6:53704600-53710800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr6:53704800-53711600	Weak transcription	Brain Germinal Matrix	brain
18	chr6:53705400-53718800	Weak transcription	NHEK	skin
19	chr6:53706000-53710400	Weak transcription	Brain Substantia Nigra	brain
20	chr6:53706000-53720200	Weak transcription	Esophagus	oesophagus
21	chr6:53706000-53722400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:53706200-53712200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:53706200-53722000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr6:53706400-53714400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr6:53706400-53720200	Weak transcription	Fetal Muscle Leg	muscle
26	chr6:53706800-53710600	Enhancers	Dnd41	blood
27	chr6:53707200-53710400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr6:53707600-53718800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr6:53707800-53710800	Weak transcription	Brain Angular Gyrus	brain
30	chr6:53707800-53712800	Weak transcription	Placenta	Placenta
31	chr6:53707800-53718800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:53708000-53712400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr6:53708400-53711200	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr6:53708600-53711400	Enhancers	Thymus	Thymus
35	chr6:53708600-53712400	Weak transcription	Small Intestine	intestine
36	chr6:53708800-53710600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr6:53709400-53718600	Weak transcription	Gastric	stomach
38	chr6:53709600-53710600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr6:53709600-53710600	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr6:53709600-53710600	Weak transcription	Fetal Intestine Large	intestine
41	chr6:53709600-53711800	Weak transcription	HepG2	liver
42	chr6:53709600-53719800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr6:53709800-53710800	Weak transcription	Brain Anterior Caudate	brain
44	chr6:53709800-53719800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr6:53709800-53762200	Weak transcription	Primary B cells from cord blood	blood
46	chr6:53710000-53710800	Enhancers	H9 Cell Line	embryonic stem cell
47	chr6:53710200-53710800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:53710200-53711000	Genic enhancers	Fetal Intestine Small	intestine
49	chr6:53710200-53711000	Flanking Active TSS	Fetal Thymus	thymus
50	chr6:53710200-53711200	Enhancers	Primary T cells from cord blood	blood

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