Variant report

Variant	rs9394395
Chromosome Location	chr6:36974668-36974669
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36952318..36954994-chr6:36973559..36976188,4	MCF-7	breast:
2	chr6:36952074..36956895-chr6:36967839..36978010,11	MCF-7	breast:
3	chr6:36952367..36954774-chr6:36974334..36977230,2	K562	blood:

Variant related genes	Relation type
ENSG00000137409	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11967185	0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[ASN][1000 genomes]
rs1724088	0.95[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs1753288	0.82[ASN][1000 genomes]
rs1753290	0.82[CEU][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs1753291	0.83[CEU][hapmap];0.86[JPT][hapmap]
rs2770122	0.88[CEU][hapmap];0.95[JPT][hapmap]
rs4714032	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.96[LWK][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs831510	0.95[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs831511	0.91[ASN][1000 genomes]
rs831512	0.95[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv885815	chr6:36915906-36979583	Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv518386	chr6:36942746-37037670	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv602952	chr6:36951210-36978745	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv885816	chr6:36965099-36999682	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9394395	SRSF3	cis	parietal	SCAN
rs9394395	STK38	cis	cerebellum	SCAN
rs9394395	PI16	cis	parietal	SCAN
rs9394395	FGD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36966800-36975000	Weak transcription	Psoas Muscle	Psoas
2	chr6:36972200-36976000	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr6:36972800-36976000	Enhancers	Primary hematopoietic stem cells	blood
4	chr6:36973000-36976000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
5	chr6:36973000-36976400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
6	chr6:36973200-36974800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr6:36973200-36976600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr6:36973400-36974800	Active TSS	Brain Substantia Nigra	brain
9	chr6:36973400-36974800	Active TSS	Placenta	Placenta
10	chr6:36973400-36974800	Active TSS	Left Ventricle	heart
11	chr6:36973400-36975200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr6:36973400-36975400	Active TSS	Fetal Stomach	stomach
13	chr6:36973400-36975800	Active TSS	Fetal Muscle Leg	muscle
14	chr6:36973400-36976200	Active TSS	Adipose Nuclei	Adipose
15	chr6:36973400-36976200	Active TSS	Brain Anterior Caudate	brain
16	chr6:36973400-36976200	Active TSS	Brain Hippocampus Middle	brain
17	chr6:36973400-36976200	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr6:36973400-36976200	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
19	chr6:36973400-36976200	Active TSS	Rectal Mucosa Donor 29	rectum
20	chr6:36973400-36976200	Active TSS	Rectal Smooth Muscle	rectum
21	chr6:36973600-36974800	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr6:36973600-36975000	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr6:36973600-36975200	Active TSS	Liver	Liver
24	chr6:36973600-36975600	Active TSS	Thymus	Thymus
25	chr6:36973600-36976800	Active TSS	Stomach Smooth Muscle	stomach
26	chr6:36973800-36974800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
27	chr6:36973800-36974800	Enhancers	Pancreas	Pancrea
28	chr6:36973800-36975000	Active TSS	Colon Smooth Muscle	Colon
29	chr6:36973800-36975000	Active TSS	Fetal Intestine Small	intestine
30	chr6:36973800-36975400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr6:36973800-36975400	Enhancers	Gastric	stomach
32	chr6:36973800-36975400	Active TSS	Spleen	Spleen
33	chr6:36973800-36975800	Active TSS	Rectal Mucosa Donor 31	rectum
34	chr6:36974000-36974800	Active TSS	Fetal Thymus	thymus
35	chr6:36974000-36975600	Enhancers	Esophagus	oesophagus
36	chr6:36974000-36975600	Enhancers	Stomach Mucosa	stomach
37	chr6:36974000-36975800	Active TSS	Colonic Mucosa	Colon
38	chr6:36974000-36976000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr6:36974200-36975000	Enhancers	Osteobl	bone
40	chr6:36974200-36975200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:36974200-36975200	Enhancers	Fetal Heart	heart
42	chr6:36974200-36975400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:36974200-36976200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr6:36974200-36976200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
45	chr6:36974200-36987000	Weak transcription	Right Atrium	heart
46	chr6:36974400-36974800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr6:36974400-36974800	Enhancers	Primary T cells fromperipheralblood	blood
48	chr6:36974400-36974800	Enhancers	Right Ventricle	heart
49	chr6:36974400-36975000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr6:36974400-36975200	Enhancers	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links