Variant report

Variant	rs3805494
Chromosome Location	chr5:40782914-40782915
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:40780330..40783240-chr5:40783326..40786085,3	K562	blood:
2	chr5:40750372..40752600-chr5:40782436..40785155,2	K562	blood:
3	chr5:40776304..40779172-chr5:40780359..40783099,2	MCF-7	breast:
4	chr5:40779894..40785582-chr5:40828129..40833355,6	K562	blood:
5	chr5:40779573..40785197-chr5:40796111..40799754,6	MCF-7	breast:
6	chr5:40773991..40776066-chr5:40782651..40784458,2	K562	blood:
7	chr5:40782479..40785312-chr5:40834773..40836537,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000212296	Chromatin interaction
ENSG00000132356	Chromatin interaction
ENSG00000145592	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10035235	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10053664	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10062565	0.84[GIH][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];1.00[YRI][hapmap]
rs10066459	0.94[JPT][hapmap]
rs10069737	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap]
rs1015027	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap]
rs10941525	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap]
rs11747210	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs12514352	0.94[ASN][1000 genomes]
rs12517210	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12518018	0.80[EUR][1000 genomes]
rs12520058	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs12523329	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1363847	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2270625	0.84[GIH][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs2291782	0.84[GIH][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];1.00[YRI][hapmap]
rs3792824	0.95[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3792827	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs3805489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3805490	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3805492	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805498	0.81[EUR][1000 genomes]
rs3805499	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes]
rs3816959	0.89[JPT][hapmap]
rs4957334	0.94[JPT][hapmap]
rs4957350	0.97[ASN][1000 genomes]
rs62357564	0.94[ASN][1000 genomes]
rs6868112	0.90[JPT][hapmap]
rs7719692	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs7721093	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs7725810	0.90[JPT][hapmap]
rs9800106	0.97[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

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40756200-40797200	Weak transcription	Gastric	stomach
2	chr5:40756400-40785200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:40756400-40797400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:40765400-40796600	Weak transcription	Right Ventricle	heart
5	chr5:40765600-40796600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr5:40771600-40788600	Weak transcription	Fetal Stomach	stomach
7	chr5:40773000-40788200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr5:40776200-40797000	Weak transcription	Colonic Mucosa	Colon
9	chr5:40776400-40784800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr5:40776600-40786200	Weak transcription	GM12878-XiMat	blood
11	chr5:40776600-40787600	Weak transcription	Hela-S3	cervix
12	chr5:40776800-40784600	Weak transcription	HUVEC	blood vessel
13	chr5:40777000-40784000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr5:40777000-40784200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr5:40777000-40784400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr5:40777000-40784400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr5:40777000-40784400	Weak transcription	Fetal Kidney	kidney
18	chr5:40777000-40787800	Weak transcription	HMEC	breast
19	chr5:40777000-40788000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr5:40777000-40788200	Weak transcription	Brain Anterior Caudate	brain
21	chr5:40777000-40789400	Weak transcription	Fetal Heart	heart
22	chr5:40777000-40796600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr5:40777000-40796600	Weak transcription	Thymus	Thymus
24	chr5:40777000-40796800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr5:40777000-40797000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr5:40777200-40783000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr5:40777200-40784000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr5:40777200-40784200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr5:40777200-40786200	Weak transcription	K562	blood
30	chr5:40777200-40787800	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr5:40777200-40787800	Weak transcription	Primary B cells from cord blood	blood
32	chr5:40777200-40787800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr5:40777200-40788000	Weak transcription	Primary hematopoietic stem cells	blood
34	chr5:40777200-40788000	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr5:40777200-40788000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr5:40777200-40788200	Weak transcription	Primary T cells from cord blood	blood
37	chr5:40777200-40788200	Weak transcription	Dnd41	blood
38	chr5:40777200-40791400	Weak transcription	Brain Angular Gyrus	brain
39	chr5:40777200-40796000	Weak transcription	Lung	lung
40	chr5:40777200-40796600	Weak transcription	Fetal Thymus	thymus
41	chr5:40777200-40796800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr5:40777400-40783400	Weak transcription	Ovary	ovary
43	chr5:40777400-40787800	Weak transcription	Fetal Brain Female	brain
44	chr5:40777600-40784400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr5:40777600-40788400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr5:40777600-40789400	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr5:40777600-40792000	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr5:40777600-40792800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr5:40777600-40795200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr5:40777600-40795600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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