Variant report

Variant	rs9356478
Chromosome Location	chr6:166751416-166751417
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:166748322..166751240-chr6:166751244..166753150,2	MCF-7	breast:
2	chr6:166750705..166753304-chr6:166793796..166795469,2	K562	blood:
3	chr6:166698710..166701539-chr6:166750702..166753192,3	K562	blood:
4	chr6:166750967..166754365-chr6:166755785..166758738,3	MCF-7	breast:
5	chr6:166751208..166754791-chr6:166757264..166760335,3	MCF-7	breast:
6	chr6:166751051..166752685-chr6:166755340..166756896,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198818	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10806847	0.91[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10862	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2343590	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4470829	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4598048	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4709112	1.00[CEU][hapmap];0.90[CHD][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4710041	0.90[CHD][hapmap];0.89[MEX][hapmap];0.82[AMR][1000 genomes]
rs6909951	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6918901	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6927168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs735297	0.81[CHD][hapmap]
rs7757549	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9355572	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9356476	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9356479	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9366005	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9366006	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9366007	1.00[CEU][hapmap];0.90[CHD][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9459654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
2	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9356478	HNRNPA1P49	cis	lung	GTEx
rs9356478	SFT2D1	cis	lymphoblastoid	seeQTL
rs9356478	LOC441177	cis	parietal	SCAN
rs9356478	SFT2D1	cis	Whole Blood	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166732400-166751600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr6:166733200-166753600	Weak transcription	Fetal Heart	heart
3	chr6:166733800-166753800	Weak transcription	Hela-S3	cervix
4	chr6:166734600-166754800	Weak transcription	HUVEC	blood vessel
5	chr6:166738200-166754200	Weak transcription	NH-A	brain
6	chr6:166739400-166755400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:166741400-166752400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:166742600-166754000	Weak transcription	Fetal Kidney	kidney
9	chr6:166744400-166752000	Weak transcription	Right Atrium	heart
10	chr6:166744400-166754800	Weak transcription	NHDF-Ad	bronchial
11	chr6:166745400-166754400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr6:166745400-166755000	Weak transcription	A549	lung
13	chr6:166745800-166752200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:166746000-166752000	Strong transcription	Fetal Intestine Large	intestine
15	chr6:166746200-166752800	Strong transcription	Fetal Intestine Small	intestine
16	chr6:166746200-166753800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:166746200-166754800	Genic enhancers	Primary B cells from peripheral blood	blood
18	chr6:166746400-166752600	Genic enhancers	Spleen	Spleen
19	chr6:166746600-166751800	Weak transcription	Colon Smooth Muscle	Colon
20	chr6:166746600-166752400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:166747000-166753400	Weak transcription	Fetal Brain Male	brain
22	chr6:166747200-166751800	Strong transcription	HepG2	liver
23	chr6:166747200-166752000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:166747200-166754600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:166747400-166752000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr6:166747600-166753000	Strong transcription	Fetal Muscle Leg	muscle
27	chr6:166747600-166753800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr6:166747600-166754000	Strong transcription	Fetal Stomach	stomach
29	chr6:166747800-166755000	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr6:166748000-166751800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:166748000-166752000	Weak transcription	Pancreas	Pancrea
32	chr6:166748000-166752000	Genic enhancers	Dnd41	blood
33	chr6:166748000-166752400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr6:166748000-166753000	Strong transcription	K562	blood
35	chr6:166748000-166754000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr6:166748200-166751600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr6:166748200-166751800	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr6:166748200-166751800	Strong transcription	Liver	Liver
39	chr6:166748200-166752000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr6:166748200-166752000	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr6:166748200-166752000	Genic enhancers	Primary T cells fromperipheralblood	blood
42	chr6:166748200-166752000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr6:166748200-166752000	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr6:166748200-166752400	Strong transcription	Primary B cells from cord blood	blood
45	chr6:166748200-166752400	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr6:166748200-166752800	Weak transcription	Small Intestine	intestine
47	chr6:166748200-166754400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr6:166748200-166754800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr6:166748400-166751600	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr6:166748400-166751800	Strong transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links