Variant report

Variant	rs10495258
Chromosome Location	chr1:227311310-227311311
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 140 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs10495263	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10495266	0.98[EUR][1000 genomes]
rs10495269	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10495270	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11549708	1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap]
rs11799413	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs11800062	0.93[EUR][1000 genomes]
rs11801443	0.94[EUR][1000 genomes]
rs11802395	0.98[EUR][1000 genomes]
rs11803761	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11803959	0.94[EUR][1000 genomes]
rs11805298	0.82[EUR][1000 genomes]
rs11806820	0.98[EUR][1000 genomes]
rs11806937	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11808186	0.98[EUR][1000 genomes]
rs11809998	0.95[EUR][1000 genomes]
rs12401556	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12401963	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12403195	0.95[EUR][1000 genomes]
rs12403391	0.98[EUR][1000 genomes]
rs12403833	0.90[CEU][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12403978	1.00[YRI][hapmap]
rs12404219	1.00[YRI][hapmap]
rs12404494	0.98[EUR][1000 genomes]
rs12404627	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12405122	0.94[EUR][1000 genomes]
rs12405686	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12405707	0.93[EUR][1000 genomes]
rs12405723	0.88[EUR][1000 genomes]
rs12405878	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs12407061	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12407545	0.95[EUR][1000 genomes]
rs12408437	0.98[EUR][1000 genomes]
rs12408913	0.80[AMR][1000 genomes]
rs12409816	0.92[EUR][1000 genomes]
rs12410327	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs12410337	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12410460	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12411017	0.96[EUR][1000 genomes]
rs1320493	0.96[EUR][1000 genomes]
rs1464076	0.80[AMR][1000 genomes]
rs1464077	1.00[CEU][hapmap]
rs1513600	0.98[EUR][1000 genomes]
rs1513603	0.82[EUR][1000 genomes]
rs1606549	0.80[AMR][1000 genomes]
rs16846855	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs16846874	0.98[EUR][1000 genomes]
rs16846877	0.98[EUR][1000 genomes]
rs16846908	0.98[EUR][1000 genomes]
rs16846910	0.98[EUR][1000 genomes]
rs16846911	0.98[EUR][1000 genomes]
rs16846972	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs16846985	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs16847014	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs16847035	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs16847098	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs16847107	1.00[CEU][hapmap]
rs16847492	1.00[CEU][hapmap]
rs16847634	1.00[CEU][hapmap]
rs17605533	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17851754	0.98[EUR][1000 genomes]
rs1877622	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1888831	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2090009	0.98[EUR][1000 genomes]
rs2150869	0.96[EUR][1000 genomes]
rs2150871	0.93[EUR][1000 genomes]
rs2150873	0.98[EUR][1000 genomes]
rs2183837	0.98[EUR][1000 genomes]
rs34263105	0.86[AMR][1000 genomes]
rs34400564	0.82[EUR][1000 genomes]
rs34953255	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41303115	0.98[EUR][1000 genomes]
rs4300186	1.00[CEU][hapmap]
rs4551563	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55685166	0.98[EUR][1000 genomes]
rs55865118	0.98[EUR][1000 genomes]
rs56834719	0.95[EUR][1000 genomes]
rs57513303	0.98[EUR][1000 genomes]
rs58532064	0.98[EUR][1000 genomes]
rs59116340	0.82[EUR][1000 genomes]
rs60079575	0.94[EUR][1000 genomes]
rs60291100	0.98[EUR][1000 genomes]
rs60641481	0.98[EUR][1000 genomes]
rs60866629	0.95[EUR][1000 genomes]
rs60979561	0.98[EUR][1000 genomes]
rs61522132	0.82[EUR][1000 genomes]
rs6675383	0.88[EUR][1000 genomes]
rs6696791	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6696794	0.98[EUR][1000 genomes]
rs6701743	0.95[EUR][1000 genomes]
rs6704087	1.00[YRI][hapmap]
rs73086746	0.93[EUR][1000 genomes]
rs73086752	0.93[EUR][1000 genomes]
rs73086775	0.93[EUR][1000 genomes]
rs73088658	0.82[EUR][1000 genomes]
rs73089725	0.95[EUR][1000 genomes]
rs73089747	0.95[EUR][1000 genomes]
rs73089755	0.98[EUR][1000 genomes]
rs73089760	0.98[EUR][1000 genomes]
rs73089765	0.98[EUR][1000 genomes]
rs73089770	0.98[EUR][1000 genomes]
rs73090612	0.82[EUR][1000 genomes]
rs73091738	0.98[EUR][1000 genomes]
rs73091740	0.98[EUR][1000 genomes]
rs73091742	0.98[EUR][1000 genomes]
rs73091755	0.98[EUR][1000 genomes]
rs73091759	0.98[EUR][1000 genomes]
rs73091761	0.98[EUR][1000 genomes]
rs73091774	0.98[EUR][1000 genomes]
rs73093463	0.96[EUR][1000 genomes]
rs73093495	0.96[EUR][1000 genomes]
rs73099023	0.98[EUR][1000 genomes]
rs73099026	0.98[EUR][1000 genomes]
rs73100804	0.98[EUR][1000 genomes]
rs73100814	0.98[EUR][1000 genomes]
rs73100852	0.96[EUR][1000 genomes]
rs73102915	0.96[EUR][1000 genomes]
rs73102920	0.95[EUR][1000 genomes]
rs73102930	0.95[EUR][1000 genomes]
rs73102936	0.95[EUR][1000 genomes]
rs7413768	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs74140276	0.96[EUR][1000 genomes]
rs74143321	0.92[EUR][1000 genomes]
rs7526283	1.00[CEU][hapmap]
rs7534286	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7535010	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7539037	0.82[EUR][1000 genomes]
rs7539750	0.82[EUR][1000 genomes]
rs7542505	1.00[CEU][hapmap]
rs7551556	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer 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	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv832792	chr1:227211378-227364992	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv873239	chr1:227222125-227361072	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv468227	chr1:227223736-227340790	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv549269	chr1:227223736-227340790	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv873240	chr1:227228946-227361072	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv873241	chr1:227242247-227361072	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv549270	chr1:227290139-227361072	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	esv2830098	chr1:227295716-227422234	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10495258	RHOU	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227214800-227329200	Weak transcription	Right Ventricle	heart
2	chr1:227257800-227312200	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr1:227259400-227349000	Weak transcription	Colonic Mucosa	Colon
4	chr1:227272800-227331000	Weak transcription	Lung	lung
5	chr1:227273000-227312400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:227282600-227318000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:227285600-227313800	Weak transcription	Gastric	stomach
8	chr1:227286400-227328200	Weak transcription	Brain Germinal Matrix	brain
9	chr1:227287400-227360800	Weak transcription	Psoas Muscle	Psoas
10	chr1:227288000-227326400	Weak transcription	A549	lung
11	chr1:227288200-227332400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:227288400-227343000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:227288400-227398000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:227288600-227312200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:227288600-227313000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr1:227288600-227316000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr1:227288600-227328200	Weak transcription	Fetal Stomach	stomach
18	chr1:227288600-227332400	Weak transcription	NHLF	lung
19	chr1:227288600-227333600	Weak transcription	Esophagus	oesophagus
20	chr1:227288800-227317200	Weak transcription	NHEK	skin
21	chr1:227288800-227330000	Weak transcription	NHDF-Ad	bronchial
22	chr1:227289000-227312000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:227295200-227316000	Weak transcription	Fetal Kidney	kidney
24	chr1:227295200-227346400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:227295400-227313800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:227296400-227326200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:227296600-227316400	Weak transcription	HSMMtube	muscle
28	chr1:227296600-227326200	Weak transcription	Fetal Lung	lung
29	chr1:227298600-227351800	Weak transcription	Hela-S3	cervix
30	chr1:227299200-227318800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:227299800-227313800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr1:227299800-227319600	Weak transcription	Fetal Intestine Large	intestine
33	chr1:227299800-227332600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr1:227300000-227311800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr1:227300000-227312000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:227300000-227312600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:227300000-227315800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr1:227300000-227316200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr1:227300000-227316400	Weak transcription	Osteobl	bone
40	chr1:227300000-227321800	Weak transcription	Colon Smooth Muscle	Colon
41	chr1:227300000-227325800	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr1:227300000-227326400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:227300000-227328600	Weak transcription	Fetal Brain Female	brain
44	chr1:227300000-227329200	Weak transcription	Aorta	Aorta
45	chr1:227300000-227333800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:227300000-227379800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr1:227300200-227312200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:227300200-227315200	Weak transcription	Adipose Nuclei	Adipose
49	chr1:227300200-227315600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:227300200-227315600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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