Variant report

Variant	rs12209624
Chromosome Location	chr6:80919133-80919134
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	chr6:80602215..80604082-chr6:80917282..80919253,2	K562	blood:
2	chr6:80918332..80920585-chr6:80923073..80926052,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10943698	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1359239	0.90[CHB][hapmap]
rs1408292	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1535825	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs1575541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1892475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2256531	0.95[CHB][hapmap];0.92[JPT][hapmap]
rs2298307	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2322632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2322633	1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2322635	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2476826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2490234	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2490239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2490241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2490244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2490245	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2490250	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2490251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2490253	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2505927	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2505929	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2505930	0.81[CHB][hapmap]
rs2505932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2505935	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2505939	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2505940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2505942	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2505944	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3805903	0.95[CHB][hapmap]
rs3805911	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3805913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3828753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4256394	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4706113	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs583426	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs590641	0.81[CEU][hapmap];0.95[CHB][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs643987	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs668329	0.80[EUR][1000 genomes]
rs682482	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs684251	0.95[CHB][hapmap]
rs684283	0.95[CHB][hapmap];0.80[EUR][1000 genomes]
rs686556	0.81[ASN][1000 genomes]
rs688867	1.00[CHB][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs6938280	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs742833	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7741013	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7745301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7746917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7770383	0.82[ASN][1000 genomes]
rs806783	0.84[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9294172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9341808	0.83[ASN][1000 genomes]
rs9343974	1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs9343977	0.95[CHB][hapmap]
rs9350847	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs942381	1.00[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs9448911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv830708	chr6:80844283-80996876	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv1034096	chr6:80856135-81150170	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv886309	chr6:80880138-80959885	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv886310	chr6:80880138-81025879	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv932996	chr6:80880896-81134991	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv497995	chr6:80883701-81134991	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv1033452	chr6:80888667-81000213	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80878000-80921000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr6:80882400-80935400	Weak transcription	Dnd41	blood
3	chr6:80891600-80931200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr6:80896200-80921000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:80896400-80927400	Weak transcription	Aorta	Aorta
6	chr6:80896400-80943800	Weak transcription	Right Ventricle	heart
7	chr6:80904200-80921800	Weak transcription	Fetal Thymus	thymus
8	chr6:80905600-80923800	Weak transcription	Small Intestine	intestine
9	chr6:80907400-80919800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr6:80907400-80920400	Weak transcription	Gastric	stomach
11	chr6:80907600-80920400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:80907600-80920400	Weak transcription	NHDF-Ad	bronchial
13	chr6:80907800-80919800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr6:80907800-80920400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr6:80907800-80920600	Weak transcription	HSMM	muscle
16	chr6:80907800-80920800	Weak transcription	Pancreas	Pancrea
17	chr6:80907800-80921000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr6:80908000-80920400	Weak transcription	Fetal Muscle Leg	muscle
19	chr6:80908000-80920400	Weak transcription	HSMMtube	muscle
20	chr6:80908000-80936200	Weak transcription	Fetal Lung	lung
21	chr6:80909000-80920400	Weak transcription	Left Ventricle	heart
22	chr6:80909000-80920400	Weak transcription	Psoas Muscle	Psoas
23	chr6:80909000-80940200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr6:80910000-80933400	Weak transcription	Esophagus	oesophagus
25	chr6:80911200-80924200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr6:80911400-80919400	Weak transcription	GM12878-XiMat	blood
27	chr6:80911400-80920000	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr6:80911800-80935200	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr6:80912000-80921000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr6:80913400-80919400	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr6:80913400-80923200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:80913600-80919800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr6:80913800-80920600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:80914000-80920000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:80914000-80920400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr6:80914600-80980400	Weak transcription	Ovary	ovary
37	chr6:80914800-80921000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr6:80914800-80929000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr6:80914800-80934400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr6:80914800-80938400	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr6:80914800-80938600	Weak transcription	Liver	Liver
42	chr6:80915200-80921000	Weak transcription	Primary B cells from cord blood	blood
43	chr6:80915400-80920200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr6:80915400-80938200	Weak transcription	Primary T cells from cord blood	blood
45	chr6:80915400-80942000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr6:80915800-80920000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr6:80915800-80920400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr6:80915800-80920400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr6:80915800-80956000	Weak transcription	Brain Substantia Nigra	brain
50	chr6:80916400-80919400	Weak transcription	Fetal Heart	heart

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