Variant report

Variant	rs11630843
Chromosome Location	chr15:77601610-77601611
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	chr15:77597221..77600603-chr15:77601241..77604606,4	K562	blood:

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10519164	0.85[ASN][1000 genomes]
rs10519167	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs11630837	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs11631909	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632729	0.92[JPT][hapmap]
rs11632999	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11633318	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11634056	1.00[ASN][1000 genomes]
rs11636803	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11637488	0.85[CEU][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs11638220	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs11639079	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs11639197	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs11639308	0.85[ASN][1000 genomes]
rs12899552	0.83[ASN][1000 genomes]
rs12904384	1.00[JPT][hapmap]
rs12909704	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs12910419	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs1554051	0.85[ASN][1000 genomes]
rs16968835	0.92[JPT][hapmap]
rs17382798	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17383727	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17383984	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17384406	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17385648	0.85[ASN][1000 genomes]
rs17466989	1.00[ASW][hapmap];0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs17468792	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17469276	0.83[ASN][1000 genomes]
rs17470228	0.85[ASN][1000 genomes]
rs2100054	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2864082	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34672572	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34870981	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34981488	0.82[ASN][1000 genomes]
rs35490414	0.85[ASN][1000 genomes]
rs35598964	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs35902242	0.82[ASN][1000 genomes]
rs4450362	0.91[ASN][1000 genomes]
rs55716459	0.82[ASN][1000 genomes]
rs62007263	0.85[ASN][1000 genomes]
rs62008430	0.94[ASN][1000 genomes]
rs62008432	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62008434	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62008455	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs66715204	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7119	0.92[JPT][hapmap]
rs71405237	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs71407208	0.85[ASN][1000 genomes]
rs7166293	0.85[CEU][hapmap];0.92[JPT][hapmap]
rs7176254	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181345	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7182880	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8030500	0.91[ASN][1000 genomes]
rs8032071	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs8032925	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1045376	chr15:77354671-77801487	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers 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	23 gene(s)	inside rSNPs	diseases
3	nsv542443	chr15:77354671-77801487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription 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 target site	23 gene(s)	inside rSNPs	diseases
4	esv1832234	chr15:77451350-77694607	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1041064	chr15:77497903-77631698	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1051744	chr15:77511489-77679160	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1044270	chr15:77534919-77611256	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv542445	chr15:77534919-77611256	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	esv1830237	chr15:77535785-77694607	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv482689	chr15:77576396-77731559	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv1040430	chr15:77584375-77676957	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11630843	HMG20A	cis	parietal	SCAN
rs11630843	HMG20A	cis	cerebellum	SCAN
rs11630843	RP11-797A18.4	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77577200-77619400	Weak transcription	HSMM	muscle
2	chr15:77583000-77603600	Weak transcription	Left Ventricle	heart
3	chr15:77586800-77601800	Weak transcription	Stomach Mucosa	stomach
4	chr15:77588600-77603400	Weak transcription	Osteobl	bone
5	chr15:77592800-77604000	Weak transcription	NHDF-Ad	bronchial
6	chr15:77597400-77604800	Weak transcription	Psoas Muscle	Psoas
7	chr15:77598800-77609800	Weak transcription	Brain Angular Gyrus	brain
8	chr15:77599000-77603000	Weak transcription	Adipose Nuclei	Adipose
9	chr15:77599000-77603000	Weak transcription	A549	lung
10	chr15:77599600-77604800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr15:77599800-77603600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr15:77600200-77602200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:77600200-77605000	Weak transcription	Colon Smooth Muscle	Colon
14	chr15:77600400-77605000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr15:77600600-77602000	Enhancers	Fetal Kidney	kidney
16	chr15:77601000-77603000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr15:77601200-77603000	Enhancers	GM12878-XiMat	blood
18	chr15:77601600-77602400	Enhancers	Fetal Lung	lung
19	chr15:77601600-77602800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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