Variant report

Variant	rs10935604
Chromosome Location	chr3:145847443-145847444
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:145841734..145843545-chr3:145847343..145850022,2	MCF-7	breast:
2	chr3:145845645..145847745-chr3:145881279..145883375,2	MCF-7	breast:
3	chr3:145842696..145844403-chr3:145846645..145849074,2	MCF-7	breast:
4	chr3:145834823..145837112-chr3:145844959..145847874,2	MCF-7	breast:
5	chr3:145841131..145847641-chr3:145875218..145882802,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152952	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10935601	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10935602	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1170389	0.83[JPT][hapmap]
rs1170390	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11717610	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12485283	0.88[JPT][hapmap]
rs12492656	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13087364	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes]
rs13088180	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1375580	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1375591	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1449443	0.85[EUR][1000 genomes]
rs1449446	0.83[EUR][1000 genomes]
rs16857897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16857919	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1913186	0.82[JPT][hapmap]
rs1982382	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2175668	0.82[JPT][hapmap]
rs3762694	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3792340	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3792345	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3804663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3804667	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4611785	0.83[EUR][1000 genomes]
rs4681293	0.83[EUR][1000 genomes]
rs4681297	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56686359	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6771106	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6771118	0.95[CEU][hapmap];0.93[CHB][hapmap];0.83[EUR][1000 genomes]
rs6775684	0.83[EUR][1000 genomes]
rs6781300	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6783926	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6792464	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes]
rs6794727	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7613150	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7628805	1.00[JPT][hapmap]
rs7642940	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9820945	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9836725	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs9869137	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[EUR][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	nsv525829	chr3:145614317-145863779	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv4046	chr3:145693249-145880189	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv877613	chr3:145833232-145912055	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145784600-145848800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr3:145810400-145849800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr3:145810800-145851200	Weak transcription	Brain Hippocampus Middle	brain
4	chr3:145819800-145849200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:145821000-145849800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:145827000-145855200	Weak transcription	Aorta	Aorta
7	chr3:145831400-145848400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:145832000-145870800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:145832600-145848400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:145834200-145851200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:145834400-145851400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr3:145834600-145852800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:145835200-145851200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:145835200-145852200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr3:145835600-145851200	Weak transcription	Fetal Kidney	kidney
16	chr3:145835800-145874000	Weak transcription	Psoas Muscle	Psoas
17	chr3:145836000-145852400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr3:145837000-145848800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:145837000-145852400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:145837200-145851200	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr3:145839400-145847600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:145839800-145849000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:145839800-145851400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:145840000-145852400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:145840200-145847600	Weak transcription	HSMMtube	muscle
26	chr3:145840200-145849800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr3:145840400-145874000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr3:145840600-145848600	Weak transcription	Fetal Stomach	stomach
29	chr3:145842000-145849800	Weak transcription	HMEC	breast
30	chr3:145843400-145848800	Weak transcription	Right Atrium	heart
31	chr3:145843400-145851200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr3:145843600-145848800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:145843600-145848800	Weak transcription	Ovary	ovary
34	chr3:145843600-145855200	Weak transcription	Left Ventricle	heart
35	chr3:145843600-145861200	Weak transcription	Right Ventricle	heart
36	chr3:145844000-145848000	Enhancers	HepG2	liver
37	chr3:145844000-145851200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr3:145844400-145848800	Weak transcription	NH-A	brain
39	chr3:145844400-145849600	Weak transcription	Fetal Heart	heart
40	chr3:145844600-145848600	Weak transcription	NHLF	lung
41	chr3:145844600-145856000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr3:145844600-145860600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr3:145844800-145848600	Weak transcription	HUVEC	blood vessel
44	chr3:145845000-145848600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:145845000-145848600	Enhancers	Liver	Liver
46	chr3:145845200-145850600	Enhancers	Colon Smooth Muscle	Colon
47	chr3:145845600-145849800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:145846000-145847600	Enhancers	Adipose Nuclei	Adipose
49	chr3:145846000-145847800	Enhancers	Fetal Lung	lung
50	chr3:145846000-145848000	Enhancers	Fetal Intestine Small	intestine

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