Variant report

Variant	rs2916738
Chromosome Location	chr8:6320642-6320643
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1031309	0.94[CEU][hapmap]
rs12546890	0.87[CEU][hapmap]
rs13248420	0.88[CEU][hapmap]
rs13281967	0.81[CEU][hapmap]
rs13282022	0.81[CEU][hapmap]
rs13282577	0.87[CEU][hapmap]
rs17077083	0.88[CEU][hapmap]
rs17077094	0.88[CEU][hapmap]
rs17613024	0.87[CEU][hapmap]
rs2277136	0.87[CEU][hapmap]
rs2440392	0.88[CEU][hapmap]
rs2440399	0.83[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2440400	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2440401	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2440402	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2440403	0.88[EUR][1000 genomes]
rs2442489	0.85[ASN][1000 genomes]
rs2442490	0.96[CHB][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2442492	0.83[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2442496	0.83[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2442499	0.88[EUR][1000 genomes]
rs2442500	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs2515581	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2515582	0.93[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2515583	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2515585	0.87[CEU][hapmap]
rs2515587	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2916733	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2916734	0.94[CEU][hapmap];0.83[CHB][hapmap];0.96[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2916737	1.00[CEU][hapmap];0.87[CHB][hapmap];0.96[JPT][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2916739	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2916740	0.93[CEU][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2916741	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs2916742	0.94[CEU][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2916743	0.94[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2916745	0.89[EUR][1000 genomes]
rs2916746	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs2920656	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs2920658	1.00[CEU][hapmap];0.87[CHB][hapmap];0.96[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2920659	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2920660	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs2920661	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2920662	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2920665	0.84[YRI][hapmap]
rs2920674	0.94[CEU][hapmap]
rs2922818	0.94[CEU][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2922819	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2922820	0.94[CEU][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2922822	0.80[AFR][1000 genomes]
rs2979648	0.85[YRI][hapmap]
rs2979651	0.87[EUR][1000 genomes]
rs2979652	0.94[CEU][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2979653	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2979655	0.83[CEU][hapmap];0.87[CHB][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2979656	0.96[CHB][hapmap];0.89[ASN][1000 genomes]
rs3020278	0.84[AFR][1000 genomes]
rs3020281	0.94[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6559164	0.88[CEU][hapmap]
rs7001036	0.88[EUR][1000 genomes]
rs7001056	0.89[EUR][1000 genomes]
rs7824209	0.94[CEU][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890034	chr8:5926632-6427868	Enhancers Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1021175	chr8:5965453-6880364	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1027682	chr8:6018123-6920312	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv3506199	chr8:6116693-6536592	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
5	esv3506200	chr8:6116693-6536592	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
6	nsv482828	chr8:6182711-6355710	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv890055	chr8:6237397-6351252	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv933282	chr8:6261036-6440592	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1015981	chr8:6286575-6578450	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
10	nsv1027313	chr8:6286575-6920312	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
11	nsv890056	chr8:6314486-6343727	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv890057	chr8:6317165-6427868	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv1023443	chr8:6319260-6332157	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2916738	MCPH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:6265000-6339200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr8:6287600-6344400	Weak transcription	Small Intestine	intestine
3	chr8:6301000-6338400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr8:6302800-6339800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr8:6303000-6321000	Weak transcription	Psoas Muscle	Psoas
6	chr8:6303000-6321000	Weak transcription	Hela-S3	cervix
7	chr8:6303000-6322800	Weak transcription	Ovary	ovary
8	chr8:6303000-6322800	Weak transcription	Spleen	Spleen
9	chr8:6303000-6325000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr8:6303000-6325200	Weak transcription	Pancreas	Pancrea
11	chr8:6303000-6338200	Weak transcription	Gastric	stomach
12	chr8:6303000-6338200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr8:6303000-6338400	Weak transcription	Colonic Mucosa	Colon
14	chr8:6303000-6338400	Weak transcription	Right Ventricle	heart
15	chr8:6303000-6339400	Weak transcription	Placenta	Placenta
16	chr8:6303200-6321000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr8:6303200-6322600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr8:6303200-6322800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr8:6303200-6339400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr8:6303200-6339400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr8:6303200-6340000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr8:6303400-6320800	Weak transcription	Colon Smooth Muscle	Colon
23	chr8:6303400-6321000	Weak transcription	Brain Anterior Caudate	brain
24	chr8:6303400-6321200	Weak transcription	HUVEC	blood vessel
25	chr8:6303600-6321600	Weak transcription	Brain Germinal Matrix	brain
26	chr8:6303800-6338400	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr8:6304000-6322600	Weak transcription	Fetal Brain Female	brain
28	chr8:6304000-6338000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr8:6304400-6360200	Weak transcription	Esophagus	oesophagus
30	chr8:6304600-6321200	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr8:6304800-6323000	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr8:6305800-6322800	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr8:6306200-6322800	Weak transcription	Fetal Intestine Large	intestine
34	chr8:6306200-6325400	Weak transcription	K562	blood
35	chr8:6306200-6328200	Weak transcription	Fetal Lung	lung
36	chr8:6306600-6322800	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr8:6308000-6330000	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr8:6308000-6338400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr8:6308000-6372600	Weak transcription	HMEC	breast
40	chr8:6308400-6321000	Weak transcription	Fetal Muscle Trunk	muscle
41	chr8:6312200-6338200	Weak transcription	Liver	Liver
42	chr8:6313200-6323200	Weak transcription	NHLF	lung
43	chr8:6313200-6338400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr8:6313400-6320800	Weak transcription	NH-A	brain
45	chr8:6314200-6321600	Weak transcription	Lung	lung
46	chr8:6314400-6321400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr8:6314400-6322800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr8:6314400-6338200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr8:6314400-6339600	Weak transcription	Brain Angular Gyrus	brain
50	chr8:6314600-6321600	Weak transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links