Variant report

Variant	rs10864435
Chromosome Location	chr1:9782766-9782767
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:9780124..9783096-chr1:9792051..9793928,2	K562	blood:
2	chr1:9647704..9650269-chr1:9779958..9782817,2	K562	blood:
3	chr1:9780672..9783300-chr1:9789920..9792123,3	K562	blood:
4	chr1:9746141..9751802-chr1:9775034..9783332,13	K562	blood:
5	chr1:9782219..9784206-chr1:9788877..9790888,2	MCF-7	breast:
6	chr1:9776188..9781647-chr1:9782146..9786494,11	K562	blood:
7	chr1:9778823..9786788-chr1:9787182..9791476,8	K562	blood:
8	chr1:9780963..9783653-chr1:9882559..9884595,2	K562	blood:
9	chr1:9781386..9784652-chr1:9924402..9927637,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000171603	Chromatin interaction
ENSG00000231789	Chromatin interaction
ENSG00000171608	Chromatin interaction
ENSG00000188807	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10779731	0.83[CHD][hapmap]
rs10864436	0.94[CHD][hapmap];0.83[MEX][hapmap]
rs11121484	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.92[TSI][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11121485	0.83[AMR][1000 genomes]
rs11121486	0.94[CHD][hapmap];0.81[GIH][hapmap];0.83[MEX][hapmap];0.83[AMR][1000 genomes]
rs11121493	0.82[CHD][hapmap];0.83[MEX][hapmap]
rs1141402	0.86[ASN][1000 genomes]
rs12042293	0.94[CHD][hapmap];0.81[GIH][hapmap];0.83[MEX][hapmap];0.86[AMR][1000 genomes]
rs12047054	0.83[CHD][hapmap]
rs12075554	1.00[CEU][hapmap]
rs12564733	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12566637	1.00[CEU][hapmap];0.89[MEX][hapmap]
rs12569008	0.83[CHD][hapmap]
rs1615629	0.83[CHD][hapmap]
rs1660742	0.83[CHD][hapmap];0.83[MEX][hapmap]
rs17034335	0.94[CHD][hapmap];0.81[MEX][hapmap]
rs3934934	0.92[CEU][hapmap]
rs7526958	0.83[CHD][hapmap]
rs7550295	0.94[CHD][hapmap];0.81[GIH][hapmap];0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv832203	chr1:9726632-9860209	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10864435	THAP3	cis	cerebellum	SCAN
rs10864435	TNFRSF1B	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9750600-9813000	Weak transcription	Right Atrium	heart
2	chr1:9768600-9787400	Weak transcription	Left Ventricle	heart
3	chr1:9769200-9783600	Weak transcription	Brain Angular Gyrus	brain
4	chr1:9772600-9788600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:9774600-9783400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:9775600-9783400	Strong transcription	Fetal Brain Female	brain
7	chr1:9777800-9790200	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr1:9777800-9790600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:9778200-9782800	Weak transcription	Liver	Liver
10	chr1:9778200-9783400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
11	chr1:9778200-9783400	Weak transcription	Fetal Lung	lung
12	chr1:9778400-9783000	Weak transcription	Colon Smooth Muscle	Colon
13	chr1:9778400-9783200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:9778400-9793400	Weak transcription	Fetal Kidney	kidney
15	chr1:9778600-9785200	Genic enhancers	Primary T cells from cord blood	blood
16	chr1:9778600-9788400	Genic enhancers	Primary T cells fromperipheralblood	blood
17	chr1:9778600-9790600	Weak transcription	Small Intestine	intestine
18	chr1:9778800-9785400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
19	chr1:9779000-9785400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr1:9779000-9788600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
21	chr1:9779200-9783000	Strong transcription	Adipose Nuclei	Adipose
22	chr1:9779200-9783000	Weak transcription	NHDF-Ad	bronchial
23	chr1:9779200-9786600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr1:9779200-9786800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr1:9779400-9782800	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:9779400-9783000	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr1:9779400-9785200	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr1:9779800-9782800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:9779800-9782800	Strong transcription	Aorta	Aorta
30	chr1:9779800-9783000	Strong transcription	Right Ventricle	heart
31	chr1:9779800-9783200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:9779800-9783200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:9779800-9783200	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr1:9779800-9785200	Strong transcription	Brain Cingulate Gyrus	brain
35	chr1:9780000-9783000	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr1:9780000-9784800	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr1:9780000-9790800	Weak transcription	Hela-S3	cervix
38	chr1:9780200-9783000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:9780200-9783000	Weak transcription	Pancreas	Pancrea
40	chr1:9780200-9783200	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr1:9780200-9783600	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr1:9780200-9785200	Strong transcription	Ovary	ovary
43	chr1:9780400-9783000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr1:9780400-9785000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
45	chr1:9780400-9785000	Strong transcription	Placenta Amnion	Placenta Amnion
46	chr1:9780600-9782800	Weak transcription	A549	lung
47	chr1:9780600-9783600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr1:9780600-9792600	Strong transcription	Dnd41	blood
49	chr1:9781000-9783000	Strong transcription	Fetal Muscle Leg	muscle
50	chr1:9781000-9785200	Strong transcription	Rectal Mucosa Donor 29	rectum

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