Variant report

Variant	rs3805489
Chromosome Location	chr5:40793344-40793345
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:40793097-40793968	K562	blood:	n/a	n/a
2	BACH1	chr5:40793254-40793432	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:40790254..40794130-chr5:40832238..40836861,6	MCF-7	breast:
2	chr5:40785220..40789232-chr5:40791780..40795190,3	K562	blood:

Variant related genes	Relation type
ENSG00000212567	TF binding region
ENSG00000145592	Chromatin interaction
ENSG00000212296	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10035235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs10053664	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10062565	0.89[JPT][hapmap];1.00[YRI][hapmap]
rs10066459	0.94[JPT][hapmap]
rs10069737	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs1015027	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs10941525	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs11747210	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12514352	0.96[ASN][1000 genomes]
rs12517210	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12520058	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs12523329	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1363847	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2270625	0.89[JPT][hapmap];1.00[YRI][hapmap]
rs2291782	0.89[JPT][hapmap];1.00[YRI][hapmap]
rs3792824	0.90[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3792827	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs3805490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3805494	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]
rs3805499	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs3816959	0.89[JPT][hapmap]
rs4957334	0.94[JPT][hapmap]
rs4957350	0.95[ASN][1000 genomes]
rs62357564	0.96[ASN][1000 genomes]
rs6868112	0.89[JPT][hapmap]
rs72747952	0.81[EUR][1000 genomes]
rs7719692	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs7721093	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs7725810	0.89[JPT][hapmap]
rs9800106	0.95[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:108 , 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	chr5:40777200-40796000	Weak transcription	Lung	lung
11	chr5:40777200-40796600	Weak transcription	Fetal Thymus	thymus
12	chr5:40777200-40796800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr5:40777600-40795200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr5:40777600-40795600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr5:40777800-40795600	Weak transcription	Primary B cells from peripheral blood	blood
16	chr5:40777800-40796600	Weak transcription	NH-A	brain
17	chr5:40778000-40795400	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr5:40781000-40796800	Weak transcription	Aorta	Aorta
19	chr5:40782400-40795600	Weak transcription	NHLF	lung
20	chr5:40783000-40795600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr5:40783800-40795600	Weak transcription	Ovary	ovary
22	chr5:40785000-40795400	Weak transcription	Pancreas	Pancrea
23	chr5:40785200-40795200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr5:40786200-40795600	Weak transcription	Psoas Muscle	Psoas
25	chr5:40788200-40794400	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr5:40788200-40795200	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr5:40788400-40796600	Weak transcription	Brain Anterior Caudate	brain
28	chr5:40788600-40795600	Weak transcription	NHDF-Ad	bronchial
29	chr5:40788600-40796000	Weak transcription	Fetal Lung	lung
30	chr5:40788600-40796600	Weak transcription	Fetal Kidney	kidney
31	chr5:40788800-40795200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr5:40788800-40795200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr5:40788800-40795200	Weak transcription	Fetal Muscle Trunk	muscle
34	chr5:40788800-40796400	Weak transcription	Fetal Brain Female	brain
35	chr5:40788800-40796400	Weak transcription	Fetal Muscle Leg	muscle
36	chr5:40788800-40796600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr5:40788800-40796600	Weak transcription	Fetal Stomach	stomach
38	chr5:40788800-40797400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr5:40789000-40793400	Weak transcription	GM12878-XiMat	blood
40	chr5:40789000-40795600	Weak transcription	Dnd41	blood
41	chr5:40789000-40796000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr5:40789000-40796600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr5:40789200-40796600	Weak transcription	Brain Germinal Matrix	brain
44	chr5:40789400-40794600	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr5:40789600-40793400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr5:40789600-40796600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr5:40789800-40794400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr5:40789800-40796800	Weak transcription	Fetal Heart	heart
49	chr5:40790000-40795600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:40790400-40794600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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