Variant report

Variant	rs10074991
Chromosome Location	chr5:40790551-40790552
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:40790254..40794130-chr5:40832238..40836861,6	MCF-7	breast:
2	chr5:40789707..40791650-chr5:40833757..40835320,2	K562	blood:

Variant related genes	Relation type
ENSG00000212296	Chromatin interaction
ENSG00000145592	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1001684	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs1002423	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1002424	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10041430	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs10065570	0.87[JPT][hapmap];0.82[YRI][hapmap]
rs10071679	0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1122655	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11956019	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11956047	0.90[AMR][1000 genomes]
rs13361707	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[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]
rs1345778	0.90[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap]
rs2329353	0.90[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28544962	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3805487	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805495	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3805497	0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4957352	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58692207	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58751240	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59133000	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59338019	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59585832	0.97[ASN][1000 genomes]
rs6868517	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6876367	0.87[JPT][hapmap];0.82[YRI][hapmap]
rs6899032	0.87[JPT][hapmap]
rs7702883	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7705504	0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv881377	chr5:40753877-40810426	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv881070	chr5:40753877-40827307	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS 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	23 gene(s)	inside rSNPs	diseases
3	nsv880438	chr5:40753877-40900717	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10074991	NUP155	cis	parietal	SCAN
rs10074991	FGF10	cis	cerebellum	SCAN
rs10074991	RPL37	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40756200-40797200	Weak transcription	Gastric	stomach
2	chr5:40756400-40797400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:40765400-40796600	Weak transcription	Right Ventricle	heart
4	chr5:40765600-40796600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr5:40776200-40797000	Weak transcription	Colonic Mucosa	Colon
6	chr5:40777000-40796600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr5:40777000-40796600	Weak transcription	Thymus	Thymus
8	chr5:40777000-40796800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr5:40777000-40797000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr5:40777200-40791400	Weak transcription	Brain Angular Gyrus	brain
11	chr5:40777200-40796000	Weak transcription	Lung	lung
12	chr5:40777200-40796600	Weak transcription	Fetal Thymus	thymus
13	chr5:40777200-40796800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr5:40777600-40792000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr5:40777600-40792800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr5:40777600-40795200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr5:40777600-40795600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr5:40777800-40795600	Weak transcription	Primary B cells from peripheral blood	blood
19	chr5:40777800-40796600	Weak transcription	NH-A	brain
20	chr5:40778000-40795400	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr5:40781000-40791200	Weak transcription	NHEK	skin
22	chr5:40781000-40796800	Weak transcription	Aorta	Aorta
23	chr5:40782400-40791400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr5:40782400-40795600	Weak transcription	NHLF	lung
25	chr5:40782600-40791200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr5:40782600-40791200	Weak transcription	Colon Smooth Muscle	Colon
27	chr5:40783000-40795600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr5:40783800-40795600	Weak transcription	Ovary	ovary
29	chr5:40785000-40792800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr5:40785000-40795400	Weak transcription	Pancreas	Pancrea
31	chr5:40785200-40795200	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr5:40786000-40791000	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr5:40786000-40791000	Weak transcription	Fetal Intestine Large	intestine
34	chr5:40786000-40791000	Weak transcription	Small Intestine	intestine
35	chr5:40786000-40791400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr5:40786200-40795600	Weak transcription	Psoas Muscle	Psoas
37	chr5:40787200-40790600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr5:40787800-40791200	Enhancers	HepG2	liver
39	chr5:40787800-40791400	Enhancers	Liver	Liver
40	chr5:40788200-40794400	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr5:40788200-40795200	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr5:40788400-40790600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr5:40788400-40791400	Weak transcription	Brain Hippocampus Middle	brain
44	chr5:40788400-40791400	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr5:40788400-40796600	Weak transcription	Brain Anterior Caudate	brain
46	chr5:40788600-40791000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr5:40788600-40791000	Weak transcription	Primary T cells from cord blood	blood
48	chr5:40788600-40791000	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr5:40788600-40791200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr5:40788600-40791200	Weak transcription	HMEC	breast

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