Variant report

Variant	rs61400878
Chromosome Location	chr3:136207669-136207670
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:136206783..136208726-chr3:136470130..136472323,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118007	Chromatin interaction
ENSG00000261758	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs34149860	1.00[EUR][1000 genomes]
rs55655018	1.00[EUR][1000 genomes]
rs55674785	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56043110	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56183552	1.00[EUR][1000 genomes]
rs56381882	1.00[EUR][1000 genomes]
rs57494495	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs58021491	1.00[EUR][1000 genomes]
rs58206781	1.00[EUR][1000 genomes]
rs58336248	1.00[EUR][1000 genomes]
rs58493992	1.00[EUR][1000 genomes]
rs58544452	1.00[EUR][1000 genomes]
rs58672018	0.91[AMR][1000 genomes]
rs59554065	1.00[EUR][1000 genomes]
rs59778182	1.00[EUR][1000 genomes]
rs60778309	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61160497	1.00[EUR][1000 genomes]
rs6790219	1.00[EUR][1000 genomes]
rs73863333	1.00[EUR][1000 genomes]
rs73863336	1.00[EUR][1000 genomes]
rs73863337	1.00[EUR][1000 genomes]
rs73863608	1.00[EUR][1000 genomes]
rs73863611	1.00[EUR][1000 genomes]
rs73863618	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73863622	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73863623	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73863625	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73863630	1.00[EUR][1000 genomes]
rs73863634	1.00[EUR][1000 genomes]
rs73863640	1.00[EUR][1000 genomes]
rs7613584	1.00[EUR][1000 genomes]
rs7626261	1.00[EUR][1000 genomes]
rs7646127	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv877519	chr3:136035737-136279390	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv877520	chr3:136056861-136310985	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv877521	chr3:136069286-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv877522	chr3:136088038-136241028	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv877523	chr3:136088038-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv520012	chr3:136088038-136314119	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv877524	chr3:136112109-136295283	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv877525	chr3:136112109-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv877526	chr3:136149139-136310985	ZNF genes & repeats Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	nsv877527	chr3:136182053-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136176400-136314200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:136176600-136212000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:136176600-136222800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:136176600-136224200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr3:136176600-136224400	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:136176600-136231800	Weak transcription	Psoas Muscle	Psoas
7	chr3:136176600-136240000	Weak transcription	HMEC	breast
8	chr3:136176600-136260800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:136176800-136228000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr3:136176800-136266200	Weak transcription	Hela-S3	cervix
11	chr3:136177200-136236400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:136178000-136212000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:136178400-136208200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:136178600-136220200	Weak transcription	Fetal Brain Male	brain
15	chr3:136179800-136212000	Weak transcription	Fetal Heart	heart
16	chr3:136181400-136211600	Weak transcription	A549	lung
17	chr3:136183800-136212000	Weak transcription	Lung	lung
18	chr3:136191000-136220000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr3:136191400-136209400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr3:136191400-136268000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr3:136192200-136212600	Weak transcription	Pancreas	Pancrea
22	chr3:136192200-136225600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:136192400-136252400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr3:136193800-136217200	Weak transcription	HepG2	liver
25	chr3:136193800-136231400	Weak transcription	NHLF	lung
26	chr3:136193800-136239200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr3:136194600-136212000	Weak transcription	Esophagus	oesophagus
28	chr3:136195000-136210600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:136195000-136220400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr3:136195000-136223000	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr3:136195200-136209800	Weak transcription	NHDF-Ad	bronchial
32	chr3:136195200-136210800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr3:136195200-136210800	Weak transcription	Primary B cells from peripheral blood	blood
34	chr3:136195200-136211400	Weak transcription	HSMM	muscle
35	chr3:136195200-136212200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr3:136195200-136231000	Weak transcription	Osteobl	bone
37	chr3:136195400-136209800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:136195400-136209800	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr3:136195400-136209800	Weak transcription	Placenta	Placenta
40	chr3:136195400-136211000	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr3:136195400-136211400	Weak transcription	Colon Smooth Muscle	Colon
42	chr3:136195400-136214200	Weak transcription	Spleen	Spleen
43	chr3:136195400-136215600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr3:136195400-136218200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:136195400-136231400	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr3:136195400-136232000	Weak transcription	Right Ventricle	heart
47	chr3:136195400-136241800	Weak transcription	NH-A	brain
48	chr3:136195400-136250400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr3:136195400-136278800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:136195600-136208000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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