Variant report

Variant	rs236676
Chromosome Location	chr4:88009620-88009621
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	chr4:88004411..88007536-chr4:88008930..88011901,3	K562	blood:
2	chr4:88005383..88008853-chr4:88008930..88010972,3	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10018904	0.86[ASN][1000 genomes]
rs10023056	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10029915	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10032710	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10516788	0.84[CEU][hapmap];0.94[GIH][hapmap];0.80[TSI][hapmap]
rs13120301	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs151450	0.97[ASN][1000 genomes]
rs151451	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17012234	0.84[CEU][hapmap];0.94[GIH][hapmap];0.80[TSI][hapmap]
rs17012334	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs17012512	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17605615	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17668131	0.86[ASN][1000 genomes]
rs17701999	0.84[CEU][hapmap];0.94[GIH][hapmap];0.80[TSI][hapmap]
rs17752307	0.84[CEU][hapmap]
rs1842685	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2035403	0.99[ASN][1000 genomes]
rs2061498	0.89[EUR][1000 genomes]
rs2280952	0.86[ASN][1000 genomes]
rs2280954	0.81[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs236679	0.86[ASN][1000 genomes]
rs236681	0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs3733377	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736668	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3755980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3755983	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3755985	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775209	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3775211	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3775226	0.89[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3775228	0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4693802	0.87[GIH][hapmap]
rs55982755	0.89[EUR][1000 genomes]
rs60695258	0.99[ASN][1000 genomes]
rs66477840	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6819155	0.84[CEU][hapmap];0.94[GIH][hapmap]
rs6840258	0.83[CEU][hapmap]
rs6854749	0.84[CEU][hapmap]
rs7665282	0.84[CEU][hapmap]
rs767315	0.83[CEU][hapmap]
rs7682652	0.84[CEU][hapmap]

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	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1001017	chr4:87872160-88087003	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv537166	chr4:87872160-88087003	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv999098	chr4:87899091-88016048	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv537167	chr4:87899091-88016048	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	nsv879525	chr4:87964363-88033352	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs236676	HSD17B13	cis	cerebellum	SCAN
rs236676	HSD17B13	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87995200-88010600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr4:87995200-88029200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:87995400-88037800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr4:87995600-88011200	Weak transcription	Colonic Mucosa	Colon
5	chr4:87995800-88023800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr4:87996800-88023600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr4:87999400-88010600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr4:87999600-88010600	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr4:87999600-88011000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:88000200-88010600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr4:88000400-88020800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:88000600-88013000	Weak transcription	A549	lung
13	chr4:88001200-88011400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr4:88001400-88013800	Weak transcription	HSMM	muscle
15	chr4:88001400-88025200	Weak transcription	Fetal Muscle Leg	muscle
16	chr4:88001600-88014000	Weak transcription	Small Intestine	intestine
17	chr4:88001800-88010600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr4:88001800-88011800	Weak transcription	Fetal Stomach	stomach
19	chr4:88001800-88013200	Weak transcription	Stomach Mucosa	stomach
20	chr4:88001800-88013400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr4:88001800-88013800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr4:88001800-88025200	Weak transcription	Gastric	stomach
23	chr4:88002000-88009800	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr4:88003400-88028600	Weak transcription	HSMMtube	muscle
25	chr4:88003600-88013000	Weak transcription	HMEC	breast
26	chr4:88003600-88013200	Weak transcription	Osteobl	bone
27	chr4:88004200-88010800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr4:88004200-88019200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr4:88004400-88025200	Weak transcription	Fetal Muscle Trunk	muscle
30	chr4:88004800-88010400	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr4:88005000-88017400	Strong transcription	Dnd41	blood
32	chr4:88005800-88014000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr4:88006200-88010600	Weak transcription	NHDF-Ad	bronchial
34	chr4:88006200-88011200	Weak transcription	Fetal Lung	lung
35	chr4:88006400-88010800	Weak transcription	K562	blood
36	chr4:88007000-88010400	Genic enhancers	Left Ventricle	heart
37	chr4:88007400-88010000	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr4:88007600-88010400	Enhancers	Right Atrium	heart
39	chr4:88007600-88014400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr4:88007600-88018200	Weak transcription	Thymus	Thymus
41	chr4:88007800-88009800	Enhancers	Brain Hippocampus Middle	brain
42	chr4:88007800-88010200	Enhancers	Brain Cingulate Gyrus	brain
43	chr4:88007800-88010600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr4:88007800-88010800	Enhancers	Right Ventricle	heart
45	chr4:88008000-88009800	Enhancers	Brain Substantia Nigra	brain
46	chr4:88008000-88010200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr4:88008000-88010200	Weak transcription	Fetal Intestine Large	intestine
48	chr4:88008000-88010600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr4:88008000-88010600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr4:88008000-88010600	Enhancers	HUVEC	blood vessel

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