Variant report

Variant	rs9402023
Chromosome Location	chr6:128543476-128543477
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1012049	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs10485160	0.84[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11961542	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11968433	0.82[YRI][hapmap]
rs12055654	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12055776	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs1543376	0.84[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs17053270	0.82[YRI][hapmap]
rs17055441	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17055472	0.83[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17055477	0.83[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2073161	0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs2076572	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3813371	0.94[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs3813372	0.93[CHB][hapmap];0.88[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3813373	0.89[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4140541	0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4243494	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4421217	0.87[ASN][1000 genomes]
rs4483000	0.84[JPT][hapmap]
rs4557544	1.00[CEU][hapmap]
rs4628122	1.00[CEU][hapmap]
rs4897252	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs61583694	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6928143	0.83[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs6933029	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6938118	0.94[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs730202	0.89[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73590673	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs742736	0.83[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7753945	0.94[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs7755473	0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs7755836	0.84[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs7773849	0.84[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs9321111	1.00[CEU][hapmap]
rs9321113	0.84[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9372885	0.81[EUR][1000 genomes]
rs9372886	0.84[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9372887	0.84[JPT][hapmap]
rs9375550	0.82[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs9375551	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9375552	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9375553	1.00[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap]
rs9375554	0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs9375555	0.83[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9375556	0.84[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9375557	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9375558	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9385452	0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs9385455	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9388618	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9388619	0.87[ASN][1000 genomes]
rs9388621	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9388622	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9388623	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs9388624	0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs9388625	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9388626	0.84[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs9388627	0.84[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9398865	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap]
rs9398866	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9398867	0.84[JPT][hapmap]
rs9398868	0.83[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9402024	0.84[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs9402025	0.80[ASN][1000 genomes]
rs9402027	0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs9402028	0.80[ASN][1000 genomes]
rs9402029	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9402030	0.83[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9402031	0.80[JPT][hapmap]
rs9402032	0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs9784773	0.84[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9784880	0.89[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv886649	chr6:128399657-128808054	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv604647	chr6:128421762-128547177	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv886651	chr6:128450019-128565778	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv886653	chr6:128455539-128555805	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv886654	chr6:128471938-128555805	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128488200-128565200	Weak transcription	Fetal Stomach	stomach
2	chr6:128492600-128567800	Weak transcription	Ovary	ovary
3	chr6:128505800-128552200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr6:128506000-128561000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr6:128520400-128573800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:128522000-128560800	Weak transcription	Primary T cells from cord blood	blood
7	chr6:128523800-128543600	Weak transcription	Left Ventricle	heart
8	chr6:128527000-128543600	Weak transcription	Fetal Intestine Small	intestine
9	chr6:128527600-128561000	Weak transcription	Esophagus	oesophagus
10	chr6:128528200-128558400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr6:128528400-128561000	Weak transcription	Fetal Brain Male	brain
12	chr6:128529400-128552600	Weak transcription	Small Intestine	intestine
13	chr6:128529800-128561000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr6:128531000-128550600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr6:128531000-128562400	Weak transcription	Aorta	Aorta
16	chr6:128531200-128554600	Weak transcription	Right Ventricle	heart
17	chr6:128531200-128562400	Weak transcription	HSMMtube	muscle
18	chr6:128531200-128567800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:128531200-128573800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:128531400-128553600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr6:128532000-128545600	Weak transcription	NHEK	skin
22	chr6:128532000-128554400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:128532000-128561000	Weak transcription	Osteobl	bone
24	chr6:128532200-128553200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:128536000-128554800	Weak transcription	Brain Substantia Nigra	brain
26	chr6:128536800-128560600	Weak transcription	Fetal Lung	lung
27	chr6:128537200-128561000	Weak transcription	Fetal Muscle Leg	muscle
28	chr6:128537400-128543600	Weak transcription	Gastric	stomach
29	chr6:128537600-128573800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr6:128539800-128552400	Weak transcription	Liver	Liver
31	chr6:128539800-128558200	Weak transcription	NH-A	brain
32	chr6:128540000-128547200	Weak transcription	HMEC	breast
33	chr6:128540200-128552800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:128540200-128556600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:128540200-128559600	Weak transcription	Primary B cells from peripheral blood	blood
36	chr6:128540200-128561000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr6:128540200-128564800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr6:128540400-128545600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:128540400-128551200	Weak transcription	HSMM	muscle
40	chr6:128540400-128554400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr6:128540400-128560400	Weak transcription	Fetal Thymus	thymus
42	chr6:128540400-128560400	Weak transcription	HUVEC	blood vessel
43	chr6:128540400-128569400	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr6:128540600-128550200	Weak transcription	Fetal Intestine Large	intestine
45	chr6:128540600-128561000	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr6:128540800-128543600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr6:128540800-128562400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr6:128541000-128545400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr6:128541000-128551200	Weak transcription	Primary B cells from cord blood	blood
50	chr6:128541200-128547000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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