Variant report

Variant	rs4935736
Chromosome Location	chr10:52364756-52364757
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52356810..52366659-chr10:52378806..52385975,25	MCF-7	breast:
2	chr10:52363840..52365627-chr10:52371839..52373893,2	K562	blood:
3	chr10:52358660..52367648-chr10:52378481..52386533,25	MCF-7	breast:
4	chr10:52362637..52365036-chr10:52365893..52368621,2	K562	blood:
5	chr10:52361922..52364870-chr10:52374462..52376104,2	MCF-7	breast:
6	chr10:52352956..52355914-chr10:52362254..52364953,3	K562	blood:

Variant related genes	Relation type
ENSG00000226200	Chromatin interaction
ENSG00000198964	Chromatin interaction
ENSG00000230036	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10740762	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10763590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10826242	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006259	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3001879	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3001883	1.00[CEU][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3001885	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3011714	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4268459	0.94[EUR][1000 genomes]
rs4935734	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4935735	1.00[CEU][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4935739	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6481442	1.00[CEU][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6481461	1.00[CEU][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7067552	1.00[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7073182	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7089882	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs7090996	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7094655	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7097359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7903649	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7904101	1.00[CEU][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7908136	0.95[EUR][1000 genomes]
rs7909486	1.00[CEU][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7918559	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]

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	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription 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	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv469522	chr10:52276564-52447589	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv482564	chr10:52276564-52447589	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4935736	CSTF2T	cis	parietal	SCAN
rs4935736	PIK3C2B	trans	parietal	SCAN
rs4935736	ARHGAP22	cis	parietal	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52338000-52367000	Weak transcription	Aorta	Aorta
2	chr10:52341200-52373000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr10:52349600-52364800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr10:52358400-52367000	Enhancers	Fetal Lung	lung
5	chr10:52358800-52367800	Enhancers	Brain Hippocampus Middle	brain
6	chr10:52359400-52369200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr10:52360000-52366200	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr10:52360200-52375600	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr10:52360400-52366000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr10:52361200-52364800	Enhancers	Liver	Liver
11	chr10:52361600-52369000	Enhancers	Brain Anterior Caudate	brain
12	chr10:52362000-52365400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr10:52362000-52365400	Enhancers	Ovary	ovary
14	chr10:52362000-52368400	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr10:52362000-52368400	Enhancers	Brain Substantia Nigra	brain
16	chr10:52362200-52367400	Enhancers	Brain Cingulate Gyrus	brain
17	chr10:52362200-52372400	Weak transcription	Esophagus	oesophagus
18	chr10:52362400-52367200	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr10:52362600-52364800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr10:52362600-52364800	Enhancers	HSMM	muscle
21	chr10:52362600-52365800	Enhancers	Fetal Intestine Small	intestine
22	chr10:52362600-52366800	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr10:52362600-52368800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr10:52362800-52364800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr10:52362800-52365000	Flanking Active TSS	Fetal Heart	heart
26	chr10:52362800-52365200	Enhancers	Brain Germinal Matrix	brain
27	chr10:52362800-52365400	Enhancers	Fetal Brain Male	brain
28	chr10:52362800-52365800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr10:52362800-52366000	Enhancers	Fetal Intestine Large	intestine
30	chr10:52362800-52366200	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr10:52362800-52366200	Enhancers	Brain Angular Gyrus	brain
32	chr10:52362800-52366400	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr10:52362800-52368000	Enhancers	HepG2	liver
34	chr10:52363000-52365000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr10:52363000-52365000	Enhancers	Rectal Smooth Muscle	rectum
36	chr10:52363000-52365400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr10:52363000-52365400	Enhancers	Psoas Muscle	Psoas
38	chr10:52363000-52365400	Flanking Active TSS	Hela-S3	cervix
39	chr10:52363000-52365800	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr10:52363000-52365800	Enhancers	Small Intestine	intestine
41	chr10:52363000-52366000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr10:52363000-52368000	Enhancers	Muscle Satellite Cultured Cells	--
43	chr10:52363200-52364800	Enhancers	Osteobl	bone
44	chr10:52363200-52365000	Enhancers	Thymus	Thymus
45	chr10:52363200-52366000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr10:52363200-52366200	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr10:52363200-52368000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr10:52363200-52368000	Enhancers	Stomach Mucosa	stomach
49	chr10:52363200-52371600	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr10:52363200-52372000	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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