Variant report

Variant	rs11204824
Chromosome Location	chr1:151444333-151444334
allele	A/G
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:151444312..151446471-chr1:151475179..151477134,2	MCF-7	breast:
2	chr1:151427933..151434225-chr1:151443087..151450932,17	K562	blood:
3	chr1:151442913..151444716-chr1:151512717..151515241,2	MCF-7	breast:
4	1:151427826-151434310..1:151443030-151447169	H1-hESC	embryonic stem cell:	embryo
5	1:151443030-151447169..1:151618750-151636526	Hela-S3	cervix:
6	chr1:151429107..151437905-chr1:151438450..151450094,72	MCF-7	breast:
7	1:151443030-151447169..1:151496437-151509688	Hela-S3	cervix:
8	chr1:151443738..151446341-chr1:151470840..151473102,2	MCF-7	breast:
9	chr1:151442862..151444708-chr1:151446075..151448070,2	MCF-7	breast:
10	chr1:151441887..151444384-chr1:151490062..151492746,2	MCF-7	breast:
11	1:151270864-151283078..1:151443030-151447169	Hela-S3	cervix:
12	chr1:151429378..151433399-chr1:151443087..151448968,15	K562	blood:
13	chr1:151428774..151440655-chr1:151441400..151449246,52	MCF-7	breast:
14	1:151411623-151426875..1:151443030-151447169	H1-hESC	embryonic stem cell:	embryo
15	1:151443030-151447169..1:151516085-151535167	H1-hESC	embryonic stem cell:	embryo

No data

Variant related genes	Relation type
ENSG00000143375	Chromatin interaction
ENSG00000265753	Chromatin interaction
ENSG00000143393	Chromatin interaction
ENSG00000252840	Chromatin interaction
ENSG00000207606	Chromatin interaction
ENSG00000232536	Chromatin interaction
ENSG00000223861	Chromatin interaction
ENSG00000143367	Chromatin interaction
ENSG00000143442	Chromatin interaction
ENSG00000143376	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10736380	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10749662	0.85[EUR][1000 genomes]
rs11204807	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs11204808	0.85[EUR][1000 genomes]
rs11204809	0.84[EUR][1000 genomes]
rs11204811	0.92[CEU][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs11204815	0.86[EUR][1000 genomes]
rs11204819	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11578888	0.92[CEU][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs11583968	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11584694	0.85[EUR][1000 genomes]
rs11586376	0.82[ASN][1000 genomes]
rs11589645	0.84[EUR][1000 genomes]
rs11801791	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12025432	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12029691	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12047617	0.85[EUR][1000 genomes]
rs12068166	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12068368	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12071705	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12120726	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs12125310	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12740875	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12743850	0.84[CEU][hapmap]
rs12751531	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16833237	0.82[JPT][hapmap]
rs1887544	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1887545	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2274533	0.92[CEU][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs2274534	0.92[CEU][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs2274535	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs2479379	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2479385	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2495380	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2495391	0.84[ASW][hapmap]
rs2864122	0.85[EUR][1000 genomes]
rs3001840	0.84[ASW][hapmap]
rs3118720	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34884031	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3748550	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3976737	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs4246526	0.87[EUR][1000 genomes]
rs4246527	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes]
rs4246528	0.84[ASW][hapmap]
rs4291502	0.84[CEU][hapmap]
rs4364884	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4528122	0.92[CEU][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs4603	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4971042	0.92[CEU][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs4971043	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4971047	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs4971049	0.90[EUR][1000 genomes]
rs61400942	0.81[ASN][1000 genomes]
rs61818037	0.82[EUR][1000 genomes]
rs61818039	0.85[EUR][1000 genomes]
rs6587572	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6587573	0.85[EUR][1000 genomes]
rs6587577	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6587584	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6587585	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6684333	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6689436	0.85[EUR][1000 genomes]
rs7172	0.92[CEU][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs7542776	0.89[EUR][1000 genomes]
rs7546151	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7546933	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
2	nsv831581	chr1:151289151-151478605	Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11204824	MRPS21	cis	parietal	SCAN
rs11204824	S100A4	cis	cerebellum	SCAN
rs11204824	SELENBP1	cis	cerebellum	SCAN
rs11204824	SELENBP1	cis	Thyroid	GTEx
rs11204824	SPRR2B	cis	parietal	SCAN
rs11204824	POGZ	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151431000-151445000	Weak transcription	Spleen	Spleen
2	chr1:151432600-151445000	Weak transcription	Fetal Intestine Small	intestine
3	chr1:151432600-151445000	Weak transcription	Pancreas	Pancrea
4	chr1:151440800-151445800	Weak transcription	Gastric	stomach
5	chr1:151442800-151445400	Weak transcription	Right Atrium	heart
6	chr1:151443200-151445800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:151443200-151445800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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