Variant report

Variant	rs3956400
Chromosome Location	chr6:121519437-121519438
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10457412	0.84[AMR][1000 genomes]
rs11154014	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12209087	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1290678	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1392863	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1846865	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1891646	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1995313	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2088832	0.86[AMR][1000 genomes]
rs218867	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs391331	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4027128	0.83[AMR][1000 genomes]
rs407586	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4395765	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4412234	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4412244	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs443149	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4461766	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4498397	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs450762	0.82[AMR][1000 genomes]
rs4601176	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4946565	0.80[EUR][1000 genomes]
rs624687	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6569197	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6569200	0.80[EUR][1000 genomes]
rs6903298	0.82[EUR][1000 genomes]
rs6911380	0.82[EUR][1000 genomes]
rs6916050	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6919890	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6926502	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6928060	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6941235	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7450632	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7768058	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7771881	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9320791	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9320806	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9320807	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9320808	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9372645	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9375004	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9375013	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9375019	0.82[AMR][1000 genomes]
rs9375022	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9385193	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9387920	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9387924	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9387929	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9387939	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9387942	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9398622	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9401368	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9401372	0.83[AMR][1000 genomes]
rs9401378	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9401380	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9401382	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9401387	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9482118	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9482119	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs976611	0.82[AMR][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	nsv1023384	chr6:121235867-121683448	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv530527	chr6:121298528-121789855	ZNF genes & repeats Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv604572	chr6:121465011-121544876	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:121478800-121535400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr6:121480200-121535600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr6:121480800-121535400	Weak transcription	Fetal Intestine Large	intestine
4	chr6:121481000-121535400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr6:121487400-121556000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr6:121495200-121529400	Weak transcription	Primary B cells from cord blood	blood
7	chr6:121496800-121535400	Weak transcription	Fetal Lung	lung
8	chr6:121498600-121535400	Weak transcription	Pancreas	Pancrea
9	chr6:121499800-121535800	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr6:121500000-121529000	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr6:121502600-121529000	Weak transcription	Left Ventricle	heart
12	chr6:121502800-121521200	Weak transcription	Primary B cells from peripheral blood	blood
13	chr6:121503000-121520600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:121509600-121575400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:121511400-121535400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:121511800-121521200	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr6:121511800-121535400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr6:121512600-121522000	Weak transcription	Fetal Stomach	stomach
19	chr6:121514200-121535600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr6:121514600-121529400	Weak transcription	Ovary	ovary
21	chr6:121515000-121535800	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr6:121515200-121535400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:121515200-121535400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr6:121515400-121535400	Weak transcription	Gastric	stomach
25	chr6:121515600-121544200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr6:121515800-121532800	Weak transcription	Fetal Intestine Small	intestine
27	chr6:121516000-121535400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr6:121516000-121560200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr6:121516800-121521400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr6:121516800-121535400	Weak transcription	Esophagus	oesophagus
31	chr6:121517400-121524000	Weak transcription	Fetal Muscle Trunk	muscle
32	chr6:121517800-121535400	Weak transcription	Aorta	Aorta
33	chr6:121518000-121529000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:121518200-121535400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr6:121518600-121535400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr6:121519000-121531800	Weak transcription	Primary T cells from cord blood	blood
37	chr6:121519000-121535600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr6:121519200-121525600	Weak transcription	Dnd41	blood

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