Variant report

Variant	rs28681561
Chromosome Location	chr7:97793026-97793027
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:97762013..97763550-chr7:97791568..97793492,2	MCF-7	breast:
2	chr7:97734652..97738073-chr7:97792918..97796975,9	MCF-7	breast:
3	chr7:97787814..97789772-chr7:97791387..97793183,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164715	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10215577	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10216274	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10227681	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10230846	0.80[ASN][1000 genomes]
rs10231625	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10232153	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10241172	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10243993	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10252338	0.85[AMR][1000 genomes]
rs10256262	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10261777	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10270280	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10276472	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10282336	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10282640	0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12704966	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12704976	0.82[ASN][1000 genomes]
rs13221415	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13221480	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13228463	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13228540	0.82[EUR][1000 genomes]
rs13241860	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13247901	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1532381	0.84[ASN][1000 genomes]
rs17169317	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17169328	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17169330	0.87[ASN][1000 genomes]
rs28415802	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34320281	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34353490	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35428901	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36081491	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3735252	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6465655	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6958785	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6980318	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73404186	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7788997	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs951987	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][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	nsv1031371	chr7:97312452-98070538	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3500384	chr7:97527787-98015382	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
3	esv3500386	chr7:97527787-98015382	Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1017481	chr7:97597641-98041043	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv539031	chr7:97597641-98041043	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv1019531	chr7:97653880-98034129	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv539032	chr7:97653880-98034129	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1816676	chr7:97676259-97868033	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv831066	chr7:97726879-97890550	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv1033029	chr7:97773232-98017992	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	nsv539033	chr7:97773232-98017992	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97763400-97801000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr7:97763400-97821000	Weak transcription	NHLF	lung
3	chr7:97763600-97814200	Weak transcription	Osteobl	bone
4	chr7:97763600-97815800	Weak transcription	HSMM	muscle
5	chr7:97764000-97806200	Weak transcription	Psoas Muscle	Psoas
6	chr7:97765800-97840800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr7:97766000-97795000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr7:97766600-97798400	Weak transcription	HSMMtube	muscle
9	chr7:97768800-97807000	Weak transcription	Stomach Mucosa	stomach
10	chr7:97771800-97797800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr7:97772400-97821600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr7:97775600-97803600	Weak transcription	K562	blood
13	chr7:97781800-97808200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:97782400-97803600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr7:97782400-97819000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr7:97782400-97822000	Weak transcription	Fetal Kidney	kidney
17	chr7:97782400-97839800	Weak transcription	Fetal Brain Male	brain
18	chr7:97782600-97807400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr7:97782800-97793200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr7:97783200-97795000	Weak transcription	Esophagus	oesophagus
21	chr7:97784600-97815000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr7:97785000-97801000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr7:97785000-97804000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr7:97785200-97818600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr7:97785400-97804600	Weak transcription	NHDF-Ad	bronchial
26	chr7:97785400-97804800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr7:97785600-97804200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr7:97786400-97800800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr7:97786800-97795000	Weak transcription	Gastric	stomach
30	chr7:97786800-97800400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr7:97786800-97801200	Weak transcription	Placenta	Placenta
32	chr7:97787200-97799400	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr7:97787400-97800200	Weak transcription	Fetal Muscle Trunk	muscle
34	chr7:97787400-97800800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr7:97787400-97801000	Weak transcription	Fetal Muscle Leg	muscle
36	chr7:97787400-97808200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr7:97787400-97822000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr7:97787800-97795000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr7:97787800-97795200	Weak transcription	Ovary	ovary
40	chr7:97787800-97800400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr7:97788200-97800400	Weak transcription	Fetal Thymus	thymus
42	chr7:97788400-97793200	Weak transcription	Fetal Stomach	stomach
43	chr7:97788400-97794600	Weak transcription	Fetal Intestine Small	intestine
44	chr7:97788400-97800200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr7:97789000-97800000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr7:97789000-97803800	Weak transcription	Brain Germinal Matrix	brain
47	chr7:97789200-97794000	Weak transcription	Pancreas	Pancrea
48	chr7:97789200-97795000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr7:97789200-97795200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr7:97789200-97797600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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