Variant report

Variant	rs9462409
Chromosome Location	chr6:38160935-38160936
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38158880..38161557-chr6:38164282..38166120,2	K562	blood:
2	chr6:38116607..38119118-chr6:38160290..38163067,2	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10807190	0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10807191	1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs10807192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10947714	0.83[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs10947716	0.91[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs11754110	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs11756830	1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs12196879	0.92[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs12197001	1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs12198616	0.92[CHB][hapmap];0.91[ASN][1000 genomes]
rs12206712	0.90[CHB][hapmap]
rs13205068	0.90[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs17678747	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17678833	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2143403	1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs2235710	0.90[ASN][1000 genomes]
rs2235711	0.91[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs3800358	0.85[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3823431	0.92[ASN][1000 genomes]
rs4314486	0.90[ASN][1000 genomes]
rs4510661	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6458044	0.92[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs6938410	0.87[ASN][1000 genomes]
rs71556980	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs735117	0.90[CHB][hapmap]
rs737171	0.80[ASN][1000 genomes]
rs742537	1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs742538	1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs7742915	0.91[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs7756835	0.91[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs909998	0.90[CHB][hapmap]
rs926565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380721	0.90[ASN][1000 genomes]
rs9462400	0.89[ASN][1000 genomes]
rs9462404	0.84[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs9462405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9462406	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9470807	0.81[CHB][hapmap]
rs9470811	0.91[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs9470813	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs9470816	1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs9470818	1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs9470819	0.89[ASN][1000 genomes]
rs9470820	0.89[ASN][1000 genomes]
rs9470822	1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs9470823	1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs9470824	0.89[ASN][1000 genomes]
rs9470825	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv522522	chr6:38131442-38207636	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv885819	chr6:38148770-38190439	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv520053	chr6:38154941-38207636	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38123400-38176800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr6:38131800-38167800	Weak transcription	Right Atrium	heart
3	chr6:38133600-38164000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:38138600-38169400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr6:38141600-38166200	Weak transcription	Left Ventricle	heart
6	chr6:38141800-38168000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr6:38142800-38162000	Weak transcription	Adipose Nuclei	Adipose
8	chr6:38143200-38161200	Weak transcription	Placenta	Placenta
9	chr6:38143600-38162400	Weak transcription	Right Ventricle	heart
10	chr6:38143600-38177200	Weak transcription	Ovary	ovary
11	chr6:38144000-38161400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:38144000-38161400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr6:38144000-38161600	Weak transcription	Thymus	Thymus
14	chr6:38145200-38163400	Weak transcription	Colonic Mucosa	Colon
15	chr6:38146000-38162400	Weak transcription	Pancreas	Pancrea
16	chr6:38146400-38161600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr6:38146400-38162400	Weak transcription	Gastric	stomach
18	chr6:38146600-38162400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr6:38147400-38180400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr6:38148200-38162200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr6:38152000-38161200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr6:38152000-38166600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr6:38153800-38161200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr6:38153800-38161400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr6:38153800-38164400	Weak transcription	Primary B cells from cord blood	blood
26	chr6:38154400-38162000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr6:38155600-38162000	Weak transcription	Brain Cingulate Gyrus	brain
28	chr6:38155600-38177200	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr6:38155800-38161000	Weak transcription	Brain Anterior Caudate	brain
30	chr6:38155800-38161000	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr6:38155800-38162800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr6:38156000-38161000	Weak transcription	Brain Germinal Matrix	brain
33	chr6:38156000-38162400	Weak transcription	Aorta	Aorta
34	chr6:38156000-38162800	Weak transcription	Brain Substantia Nigra	brain
35	chr6:38156200-38161000	Weak transcription	Fetal Muscle Trunk	muscle
36	chr6:38157000-38162000	Weak transcription	Spleen	Spleen
37	chr6:38157800-38166200	Weak transcription	Psoas Muscle	Psoas
38	chr6:38158200-38163200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr6:38158800-38162400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr6:38159200-38161600	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr6:38159200-38161600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr6:38159200-38161800	Enhancers	H1 Cell Line	embryonic stem cell
43	chr6:38159200-38161800	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr6:38159200-38162200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr6:38159200-38162600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:38159200-38162600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr6:38159400-38161400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
48	chr6:38159400-38161800	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr6:38159400-38162000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr6:38159600-38161000	Weak transcription	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links