Variant report

Variant	rs9644681
Chromosome Location	chr8:9994504-9994505
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10104911	0.82[CHB][hapmap]
rs10107485	0.86[CHB][hapmap]
rs11249969	0.82[MEX][hapmap]
rs1160369	0.88[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.83[ASN][1000 genomes]
rs11774411	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs11783851	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs11785454	0.84[ASN][1000 genomes]
rs11998591	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs12542030	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs12545469	0.82[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs12545775	0.82[JPT][hapmap]
rs12545788	0.82[JPT][hapmap]
rs12547884	0.85[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs12549943	0.90[JPT][hapmap]
rs12674871	0.90[JPT][hapmap]
rs13249013	0.82[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.84[ASN][1000 genomes]
rs13256357	0.90[JPT][hapmap]
rs1466555	0.88[ASN][1000 genomes]
rs1484645	0.83[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1564808	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs17149332	0.82[CHB][hapmap]
rs17151108	0.82[MEX][hapmap]
rs17151140	0.87[CHB][hapmap]
rs17151142	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs17151145	0.87[CHB][hapmap];0.80[CHD][hapmap];0.82[MEX][hapmap]
rs17151147	0.87[CHB][hapmap];0.80[CHD][hapmap];0.82[MEX][hapmap]
rs17151188	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs17151190	0.83[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs17151193	0.86[CHB][hapmap];0.88[CHD][hapmap];0.82[ASN][1000 genomes]
rs17151201	0.81[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs17155393	0.82[JPT][hapmap]
rs1984863	0.82[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1994223	0.82[CHB][hapmap];0.82[MEX][hapmap]
rs1994224	0.82[CHB][hapmap]
rs2016221	0.90[ASN][1000 genomes]
rs2046398	0.86[CHB][hapmap]
rs2898242	0.88[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs4840463	0.82[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs4840464	0.81[CHB][hapmap]
rs4841280	0.82[CHB][hapmap]
rs4841283	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs62488714	0.82[ASN][1000 genomes]
rs6601417	0.91[CHB][hapmap]
rs66602888	0.85[ASN][1000 genomes]
rs685218	0.82[CHB][hapmap]
rs6985791	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7008407	0.95[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs7008695	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7012601	0.84[ASN][1000 genomes]
rs7016690	0.84[ASN][1000 genomes]
rs72626643	0.86[ASN][1000 genomes]
rs7830843	0.83[ASN][1000 genomes]
rs7843906	0.82[CHB][hapmap];0.83[CHD][hapmap];0.82[MEX][hapmap]
rs9329215	0.88[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs936749	0.81[CHB][hapmap]
rs963593	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916493	chr8:9806580-10029482	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv610263	chr8:9941021-10090149	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1034343	chr8:9948342-10014155	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv831230	chr8:9953343-10139350	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1027280	chr8:9958259-10058984	Enhancers Active TSS Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv1021921	chr8:9958259-10212555	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv1850829	chr8:9958321-10045451	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9644681	MSRA	cis	lymphoblastoid	seeQTL
rs9644681	MFHAS1	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:9970600-9995800	Weak transcription	Pancreas	Pancrea
2	chr8:9986200-10002200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr8:9987200-9995800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr8:9988800-9996200	Weak transcription	Brain Hippocampus Middle	brain
5	chr8:9988800-10002200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr8:9989000-9995000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr8:9989000-9995200	Weak transcription	Brain Angular Gyrus	brain
8	chr8:9989000-10000400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr8:9991200-9997600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr8:9991200-10004600	Weak transcription	Esophagus	oesophagus
11	chr8:9991600-9996000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr8:9991800-9995800	Enhancers	Fetal Brain Female	brain
13	chr8:9992000-9997400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr8:9992200-9995200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr8:9992200-9995200	Weak transcription	Fetal Intestine Small	intestine
16	chr8:9992200-9995400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr8:9992200-9995800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr8:9992200-9995800	Weak transcription	Left Ventricle	heart
19	chr8:9992200-9995800	Weak transcription	Lung	lung
20	chr8:9992200-9995800	Weak transcription	Right Atrium	heart
21	chr8:9992200-10004800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr8:9992200-10004800	Weak transcription	Right Ventricle	heart
23	chr8:9992400-10000600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr8:9992600-9995200	Weak transcription	Brain Germinal Matrix	brain
25	chr8:9992600-9995400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr8:9992600-9995800	Weak transcription	Brain Anterior Caudate	brain
27	chr8:9992600-9995800	Weak transcription	Fetal Heart	heart
28	chr8:9992600-9996200	Weak transcription	Brain Substantia Nigra	brain
29	chr8:9992600-10000600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr8:9992800-9994800	Weak transcription	Liver	Liver
31	chr8:9992800-9995800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr8:9993000-9995600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr8:9993400-9995400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr8:9993800-9995000	Weak transcription	Fetal Brain Male	brain
35	chr8:9994200-9995400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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