Variant report

Variant	rs2074190
Chromosome Location	chr17:45811210-45811211
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:45806529..45809285-chr17:45811210..45813410,2	MCF-7	breast:
2	chr17:45770364..45773006-chr17:45811021..45813221,2	K562	blood:
3	chr17:45811192..45813329-chr17:45818442..45821780,3	K562	blood:

Variant related genes	Relation type
ENSG00000198933	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10445375	0.82[JPT][hapmap]
rs11079786	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11079791	0.82[JPT][hapmap]
rs11655336	0.82[JPT][hapmap]
rs11657388	0.84[ASW][hapmap]
rs12451815	0.82[JPT][hapmap]
rs12950390	0.82[JPT][hapmap]
rs1989291	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4793646	0.82[JPT][hapmap]
rs4794063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4794067	0.84[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58067360	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8071192	0.82[JPT][hapmap]

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	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv908571	chr17:45765249-45821510	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
3	nsv2071	chr17:45801503-45844229	Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2074190	C17orf57	cis	parietal	SCAN
rs2074190	HAP1	cis	parietal	SCAN
rs2074190	C17orf57	cis	cerebellum	SCAN
rs2074190	SNX11	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45810000-45812200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
2	chr17:45810200-45811400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr17:45810200-45811600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr17:45810200-45811600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr17:45810200-45811600	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr17:45810200-45811800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
7	chr17:45810200-45811800	Bivalent Enhancer	Fetal Heart	heart
8	chr17:45810400-45811400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
9	chr17:45810400-45811400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr17:45810400-45811400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
11	chr17:45810400-45811400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
12	chr17:45810400-45811400	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr17:45810400-45811400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
14	chr17:45810400-45811400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr17:45810400-45811400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr17:45810400-45811400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr17:45810400-45811400	Active TSS	Right Atrium	heart
18	chr17:45810400-45811400	Bivalent/Poised TSS	A549	lung
19	chr17:45810400-45811600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
20	chr17:45810400-45811600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
21	chr17:45810400-45811600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
22	chr17:45810400-45811600	Bivalent Enhancer	Fetal Brain Male	brain
23	chr17:45810400-45811600	Bivalent/Poised TSS	Fetal Brain Female	brain
24	chr17:45810400-45811800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
25	chr17:45810400-45811800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
26	chr17:45810400-45811800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr17:45810400-45811800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr17:45810400-45812000	Active TSS	GM12878-XiMat	blood
29	chr17:45810400-45813200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr17:45810400-45813200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr17:45810400-45813400	Active TSS	Primary T killer memory cells from peripheral blood	blood
32	chr17:45810400-45814000	Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr17:45810400-45814400	Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr17:45810600-45811400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
35	chr17:45810600-45811400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr17:45810600-45811400	Bivalent/Poised TSS	Psoas Muscle	Psoas
37	chr17:45810600-45811400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
38	chr17:45810600-45811600	Bivalent/Poised TSS	Small Intestine	intestine
39	chr17:45810600-45811800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr17:45810600-45812200	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
41	chr17:45810600-45813000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr17:45810800-45811400	Bivalent Enhancer	Brain Cingulate Gyrus	brain
43	chr17:45810800-45811400	Bivalent/Poised TSS	Esophagus	oesophagus
44	chr17:45810800-45811400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
45	chr17:45810800-45811400	Active TSS	Ovary	ovary
46	chr17:45810800-45811400	Flanking Active TSS	Right Ventricle	heart
47	chr17:45810800-45811600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
48	chr17:45810800-45811600	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
49	chr17:45810800-45811600	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
50	chr17:45810800-45811800	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood

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