Variant report

Variant	rs9993675
Chromosome Location	chr4:56243522-56243523
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:56240281..56248484-chr4:56258541..56264383,10	MCF-7	breast:
2	chr4:56243121..56245532-chr4:56269359..56271036,2	MCF-7	breast:
3	chr4:56243246..56246194-chr4:56252558..56255228,2	K562	blood:
4	chr4:56232345..56235244-chr4:56243502..56246293,2	MCF-7	breast:
5	chr4:56242859..56244576-chr4:56261774..56264721,2	K562	blood:
6	chr4:56240192..56241907-chr4:56242608..56245605,4	K562	blood:

Variant related genes	Relation type
ENSG00000273257	Chromatin interaction
ENSG00000249700	Chromatin interaction
ENSG00000134851	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10002541	0.92[CEU][hapmap]
rs10005989	0.91[CEU][hapmap]
rs1011095	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11133376	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11133379	0.92[CEU][hapmap]
rs11133383	0.92[CEU][hapmap];0.86[GIH][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs11133399	0.92[CEU][hapmap];0.86[GIH][hapmap];0.85[TSI][hapmap]
rs1128141	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11726609	0.92[CEU][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs11735267	0.92[CEU][hapmap]
rs11931061	0.92[CEU][hapmap];0.80[GIH][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap]
rs11939815	0.92[CEU][hapmap]
rs13102385	0.92[CEU][hapmap]
rs13121235	0.91[CEU][hapmap]
rs13149568	0.81[JPT][hapmap]
rs1522106	0.92[CEU][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs1522111	0.91[CEU][hapmap]
rs2177127	0.92[CEU][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs2177129	0.92[CEU][hapmap]
rs2412643	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2412646	0.92[CEU][hapmap]
rs28665088	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28726308	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3736544	0.92[CEU][hapmap]
rs3805147	0.92[CEU][hapmap]
rs3805154	0.92[CEU][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs3817444	0.92[CEU][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap]
rs4580704	0.92[CEU][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs473005	0.92[CEU][hapmap];0.91[GIH][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap]
rs480479	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs4865010	0.92[CEU][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap]
rs501679	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs576779	0.82[EUR][1000 genomes]
rs6554286	0.96[CEU][hapmap]
rs6811520	0.92[CEU][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs6812042	0.92[CEU][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs6815516	0.92[CEU][hapmap]
rs6819649	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6824955	0.92[CEU][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs6832769	0.92[CEU][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap]
rs6837710	0.92[CEU][hapmap]
rs6851838	0.91[CEU][hapmap];0.85[CHB][hapmap]
rs6853192	0.87[CEU][hapmap]
rs726967	0.92[CEU][hapmap]
rs7660054	0.92[CEU][hapmap];0.95[GIH][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs7667849	0.92[CEU][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs7673908	0.92[CEU][hapmap];0.86[GIH][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap]
rs7684810	0.87[CEU][hapmap]
rs819271	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9312662	0.92[CEU][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs9997288	0.92[CEU][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv999477	chr4:56219035-56397180	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv537101	chr4:56219035-56397180	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9993675	SRD5A3	cis	parietal	SCAN
rs9993675	SRD5A3	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56213800-56251400	Weak transcription	Pancreas	Pancrea
2	chr4:56214400-56247600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:56225800-56244800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr4:56225800-56244800	Weak transcription	Stomach Mucosa	stomach
5	chr4:56226000-56245000	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr4:56226000-56245000	Weak transcription	HSMMtube	muscle
7	chr4:56228000-56244800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:56228400-56245400	Weak transcription	K562	blood
9	chr4:56228400-56251000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr4:56230600-56245200	Weak transcription	Fetal Intestine Small	intestine
11	chr4:56232000-56247600	Weak transcription	Spleen	Spleen
12	chr4:56233200-56261600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr4:56234000-56244800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:56235800-56247600	Weak transcription	Aorta	Aorta
15	chr4:56236400-56248400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr4:56236800-56243800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr4:56237000-56245400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:56237000-56247800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr4:56237200-56247800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr4:56239000-56245000	Weak transcription	Adipose Nuclei	Adipose
21	chr4:56239800-56251400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr4:56240200-56249400	Weak transcription	Left Ventricle	heart
23	chr4:56240400-56259600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr4:56240600-56243600	Weak transcription	Brain Substantia Nigra	brain
25	chr4:56240600-56243800	Weak transcription	Brain Hippocampus Middle	brain
26	chr4:56240800-56247400	Weak transcription	Brain Angular Gyrus	brain
27	chr4:56241200-56244600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr4:56243200-56243800	Enhancers	Brain Cingulate Gyrus	brain
29	chr4:56243200-56244000	Enhancers	Brain Anterior Caudate	brain
30	chr4:56243400-56244200	Enhancers	Brain Inferior Temporal Lobe	brain

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