Variant report

Variant	rs9865193
Chromosome Location	chr3:119734607-119734608
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	chr3:119729710..119735147-chr3:119812192..119816098,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000082701	Chromatin interaction
ENSG00000242622	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1037974	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13314836	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13322562	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17246730	1.00[ASN][1000 genomes]
rs17246737	1.00[ASW][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1903764	1.00[ASN][1000 genomes]
rs28821007	1.00[ASW][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34002644	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3732358	1.00[JPT][hapmap]
rs3755556	1.00[JPT][hapmap]
rs4491944	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs57027844	1.00[ASN][1000 genomes]
rs57132942	1.00[ASN][1000 genomes]
rs58299321	1.00[ASN][1000 genomes]
rs58371446	1.00[ASN][1000 genomes]
rs58991487	1.00[ASN][1000 genomes]
rs59368677	1.00[ASN][1000 genomes]
rs59703574	0.86[ASN][1000 genomes]
rs60049973	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60325644	1.00[ASN][1000 genomes]
rs60993278	1.00[ASN][1000 genomes]
rs61188334	1.00[ASN][1000 genomes]
rs61511292	1.00[ASN][1000 genomes]
rs61566983	1.00[ASN][1000 genomes]
rs6796550	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs922337	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9812146	1.00[YRI][hapmap]
rs9812149	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9834346	1.00[ASW][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9843795	1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9849889	1.00[ASW][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs9853463	1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs9867915	1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9872321	1.00[ASW][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][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	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119712600-119745000	Weak transcription	Hela-S3	cervix
2	chr3:119713200-119744400	Weak transcription	Fetal Kidney	kidney
3	chr3:119718200-119736800	Weak transcription	Liver	Liver
4	chr3:119720200-119736600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:119720200-119741000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr3:119720400-119737200	Weak transcription	NHDF-Ad	bronchial
7	chr3:119720800-119738600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr3:119723200-119734800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:119723200-119736200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:119723600-119740600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:119724000-119736800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr3:119724000-119738200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr3:119724000-119741400	Weak transcription	Thymus	Thymus
14	chr3:119730000-119743000	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr3:119730000-119743000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:119730600-119736200	Weak transcription	Stomach Mucosa	stomach
17	chr3:119730600-119736400	Weak transcription	Small Intestine	intestine
18	chr3:119730600-119739200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:119730600-119740800	Weak transcription	Left Ventricle	heart
20	chr3:119730600-119741600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr3:119730800-119736800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr3:119731000-119741400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:119731200-119736800	Weak transcription	Adipose Nuclei	Adipose
24	chr3:119731400-119752400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:119731600-119737200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr3:119731800-119737000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr3:119731800-119739800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:119732000-119736200	Weak transcription	Psoas Muscle	Psoas
29	chr3:119732000-119739400	Weak transcription	Ovary	ovary
30	chr3:119732200-119747200	Weak transcription	Gastric	stomach
31	chr3:119732200-119747600	Weak transcription	Right Ventricle	heart
32	chr3:119732400-119736400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr3:119732600-119734800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:119732600-119734800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr3:119732600-119735000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr3:119732600-119735000	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr3:119732600-119736200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:119732600-119736200	Weak transcription	Colon Smooth Muscle	Colon
39	chr3:119732600-119736400	Weak transcription	Duodenum Mucosa	Duodenum
40	chr3:119732600-119736800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr3:119732600-119737000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:119732600-119738200	Weak transcription	Fetal Heart	heart
43	chr3:119732600-119739200	Weak transcription	Brain Anterior Caudate	brain
44	chr3:119732600-119739200	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr3:119732600-119740800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:119732600-119741600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr3:119732600-119748400	Weak transcription	Brain Angular Gyrus	brain
48	chr3:119732600-119748600	Weak transcription	HSMM	muscle
49	chr3:119732600-119757800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:119732800-119746200	Weak transcription	Fetal Lung	lung

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