Variant report

Variant	rs1209159
Chromosome Location	chr6:131509096-131509097
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11154621	1.00[CHB][hapmap]
rs11154622	1.00[CHB][hapmap]
rs11755717	1.00[CHB][hapmap]
rs11758994	1.00[CHB][hapmap]
rs1190788	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1190794	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1190796	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1190799	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1190800	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1190801	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1190802	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs1190805	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1190806	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1190809	0.86[EUR][1000 genomes]
rs1190810	0.94[EUR][1000 genomes]
rs1190812	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs13195700	1.00[CHB][hapmap]
rs13200165	1.00[CHB][hapmap]
rs13206776	1.00[CHB][hapmap]
rs1570348	1.00[CHB][hapmap]
rs1729549	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1729558	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1746469	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs1746470	1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1746471	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1746473	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1746474	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17573187	1.00[CHB][hapmap]
rs17651753	1.00[CHB][hapmap]
rs17787964	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1885641	1.00[CHB][hapmap]
rs3777474	0.92[EUR][1000 genomes]
rs3777476	1.00[CHB][hapmap]
rs3777487	1.00[CHB][hapmap]
rs3850239	0.81[AMR][1000 genomes]
rs3903759	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs4310080	1.00[CHB][hapmap]
rs4424112	1.00[CHB][hapmap]
rs56318353	1.00[ASN][1000 genomes]
rs66533103	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7743894	1.00[CHB][hapmap]
rs9492861	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs9492864	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9492865	1.00[CHB][hapmap]
rs9492869	1.00[CHB][hapmap]
rs9492874	0.83[ASN][1000 genomes]
rs9492883	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032955	chr6:131298803-131818502	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538443	chr6:131298803-131818502	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv830807	chr6:131390952-131581931	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv886664	chr6:131443843-131754930	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 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	chr6:131457600-131520800	Weak transcription	Right Ventricle	heart
2	chr6:131458200-131513400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr6:131484400-131509200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:131485400-131509600	Weak transcription	Small Intestine	intestine
5	chr6:131485600-131514000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr6:131487000-131512800	Weak transcription	Brain Hippocampus Middle	brain
7	chr6:131488200-131534800	Weak transcription	Gastric	stomach
8	chr6:131489000-131513000	Weak transcription	Colon Smooth Muscle	Colon
9	chr6:131494800-131514000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:131504200-131514000	Weak transcription	Brain Germinal Matrix	brain
11	chr6:131504600-131512800	Weak transcription	Brain Angular Gyrus	brain
12	chr6:131505000-131512000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:131505000-131518800	Weak transcription	Thymus	Thymus
14	chr6:131505000-131521000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:131505000-131521800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:131505200-131512800	Weak transcription	Aorta	Aorta
17	chr6:131505200-131513400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr6:131505200-131522600	Weak transcription	HSMMtube	muscle
19	chr6:131505800-131534600	Weak transcription	Brain Substantia Nigra	brain
20	chr6:131505800-131534800	Weak transcription	Pancreas	Pancrea
21	chr6:131506000-131515800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr6:131506200-131512800	Weak transcription	Left Ventricle	heart
23	chr6:131506400-131510000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:131506400-131512600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr6:131506400-131512800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr6:131506400-131512800	Weak transcription	Placenta	Placenta
27	chr6:131506400-131512800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr6:131506400-131520800	Weak transcription	Duodenum Mucosa	Duodenum
29	chr6:131506600-131512800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr6:131506600-131512800	Weak transcription	Esophagus	oesophagus
31	chr6:131506600-131512800	Weak transcription	Fetal Intestine Small	intestine
32	chr6:131506600-131512800	Weak transcription	Fetal Muscle Leg	muscle
33	chr6:131506600-131512800	Weak transcription	Fetal Stomach	stomach
34	chr6:131506600-131514200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr6:131506600-131520600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:131506600-131520600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr6:131506600-131520600	Weak transcription	Spleen	Spleen
38	chr6:131506600-131520800	Weak transcription	Lung	lung
39	chr6:131506600-131523800	Weak transcription	HepG2	liver
40	chr6:131506600-131524000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr6:131506600-131529800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr6:131506600-131532000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:131506800-131509800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr6:131506800-131510400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr6:131506800-131512000	Weak transcription	Adipose Nuclei	Adipose
46	chr6:131506800-131512600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr6:131506800-131512600	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr6:131506800-131512800	Weak transcription	Brain Anterior Caudate	brain
49	chr6:131506800-131512800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr6:131506800-131512800	Weak transcription	Fetal Muscle Trunk	muscle

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