Variant report

Variant	rs7621259
Chromosome Location	chr3:119224113-119224114
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	chr3:119181035..119182773-chr3:119221780..119224336,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176142	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1060569	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13080905	0.94[ASN][1000 genomes]
rs1797839	0.91[ASN][1000 genomes]
rs1900742	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1919586	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1919590	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1967621	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1976919	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2030816	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2177812	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732413	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3814397	0.91[ASN][1000 genomes]
rs4687855	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687860	0.94[ASN][1000 genomes]
rs4688005	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4688007	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4688008	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688012	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688014	0.89[ASN][1000 genomes]
rs6414282	0.91[ASN][1000 genomes]
rs6414283	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6438528	0.94[ASN][1000 genomes]
rs6438529	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6438530	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6438531	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6438535	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6777535	0.94[ASN][1000 genomes]
rs6778945	0.92[ASN][1000 genomes]
rs6794822	0.91[ASN][1000 genomes]
rs6796970	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs727905	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7430798	0.94[ASN][1000 genomes]
rs7628626	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7630587	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7642502	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289129	0.94[ASN][1000 genomes]
rs9809155	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9836326	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9836627	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850447	0.92[ASN][1000 genomes]
rs9867768	0.92[ASN][1000 genomes]
rs9873196	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9874480	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9877854	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119218000-119224400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:119218000-119225000	Weak transcription	Gastric	stomach
3	chr3:119218000-119231800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:119218000-119236600	Weak transcription	Aorta	Aorta
5	chr3:119218600-119224600	Weak transcription	Brain Germinal Matrix	brain
6	chr3:119218600-119225000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:119218600-119225000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:119218600-119225000	Weak transcription	Lung	lung
9	chr3:119218600-119231800	Weak transcription	Spleen	Spleen
10	chr3:119218600-119234400	Weak transcription	Colonic Mucosa	Colon
11	chr3:119218600-119236600	Weak transcription	Esophagus	oesophagus
12	chr3:119218800-119225000	Weak transcription	Thymus	Thymus
13	chr3:119218800-119233000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr3:119219000-119224600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:119219000-119235800	Weak transcription	Fetal Kidney	kidney
16	chr3:119219400-119236800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:119219600-119237000	Weak transcription	Small Intestine	intestine
18	chr3:119219800-119224600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr3:119219800-119228000	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr3:119219800-119231000	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr3:119219800-119232000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr3:119219800-119232000	Weak transcription	Brain Substantia Nigra	brain
23	chr3:119219800-119233600	Weak transcription	Ovary	ovary
24	chr3:119219800-119235800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr3:119219800-119239200	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr3:119220000-119224600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr3:119220000-119225000	Weak transcription	Pancreas	Pancrea
28	chr3:119220000-119226400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:119220000-119226600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:119220000-119226600	Weak transcription	HSMMtube	muscle
31	chr3:119220000-119231800	Weak transcription	Fetal Brain Male	brain
32	chr3:119220000-119243600	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr3:119220200-119224400	Weak transcription	Fetal Brain Female	brain
34	chr3:119220200-119226600	Weak transcription	Psoas Muscle	Psoas
35	chr3:119220200-119228200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr3:119220200-119229200	Weak transcription	HepG2	liver
37	chr3:119220200-119231800	Weak transcription	Fetal Heart	heart
38	chr3:119220200-119246800	Weak transcription	Stomach Mucosa	stomach
39	chr3:119220400-119226200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr3:119220400-119226800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr3:119220600-119225000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr3:119220600-119225600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr3:119220600-119225600	Strong transcription	Osteobl	bone
44	chr3:119220600-119228400	Strong transcription	Fetal Thymus	thymus
45	chr3:119220600-119230600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr3:119220800-119224600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr3:119220800-119225000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr3:119220800-119225200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:119220800-119226000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr3:119220800-119228000	Strong transcription	Rectal Mucosa Donor 29	rectum

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