Variant report

Variant	rs2960258
Chromosome Location	chr7:102022899-102022900
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	chr7:101927301..101930290-chr7:102022735..102024275,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160999	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10238421	0.97[ASN][1000 genomes]
rs10953364	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10953366	0.90[EUR][1000 genomes]
rs1109204	0.92[ASN][1000 genomes]
rs11444	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11496123	0.88[EUR][1000 genomes]
rs2049557	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2410988	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2410989	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2960244	0.89[ASN][1000 genomes]
rs2960248	0.80[ASN][1000 genomes]
rs2960268	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3988090	0.94[ASN][1000 genomes]
rs4338028	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4729786	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4729787	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4729788	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55743224	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55989026	0.89[ASN][1000 genomes]
rs55995033	0.92[EUR][1000 genomes]
rs58910789	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61652290	0.83[ASN][1000 genomes]
rs6955864	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6971258	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73189811	0.92[EUR][1000 genomes]
rs73189869	0.92[EUR][1000 genomes]
rs7802423	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1814780	chr7:101912320-102375950	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv1819566	chr7:101912320-102375950	Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Enhancers 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 miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv1822347	chr7:101912320-102375950	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	esv1825708	chr7:101912320-102375950	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
5	esv1842898	chr7:101912320-102375950	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	esv1847418	chr7:101912320-102375950	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
7	nsv427798	chr7:101912320-102375950	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	nsv428182	chr7:101912320-102375950	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats 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 miRNA target site	61 gene(s)	inside rSNPs	diseases
9	nsv1016563	chr7:101912320-102695860	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
10	nsv1028438	chr7:101912320-102704135	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
11	nsv1029079	chr7:101939998-102112371	Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
12	esv1818954	chr7:101957513-102328097	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	esv1828190	chr7:101966669-102439077	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
14	esv1829377	chr7:101970299-102330884	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
15	nsv831083	chr7:101981005-102295869	Active TSS Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
16	esv1806297	chr7:101981544-102330884	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
17	esv1810415	chr7:101993063-102375950	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
18	esv1811751	chr7:101993063-102375950	Enhancers Genic enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
19	esv1829118	chr7:101993063-102375950	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
20	esv1833155	chr7:101993063-102375950	Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 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	chr7:102005000-102036200	Weak transcription	Aorta	Aorta
2	chr7:102005000-102036200	Weak transcription	Small Intestine	intestine
3	chr7:102005200-102036000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr7:102005200-102036000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr7:102005400-102036000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr7:102005400-102036200	Weak transcription	Brain Angular Gyrus	brain
7	chr7:102005400-102036200	Weak transcription	Psoas Muscle	Psoas
8	chr7:102005800-102023800	Weak transcription	Primary B cells from cord blood	blood
9	chr7:102012800-102031200	Strong transcription	Fetal Muscle Leg	muscle
10	chr7:102012800-102034600	Strong transcription	Fetal Stomach	stomach
11	chr7:102013600-102035800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr7:102015400-102024000	Weak transcription	Stomach Mucosa	stomach
13	chr7:102015800-102036000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr7:102016200-102023000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr7:102016400-102028200	Strong transcription	Primary B cells from peripheral blood	blood
16	chr7:102016800-102029200	Strong transcription	Fetal Muscle Trunk	muscle
17	chr7:102017000-102027800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr7:102017200-102023000	Strong transcription	Left Ventricle	heart
19	chr7:102017200-102023200	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr7:102017200-102024600	Strong transcription	Brain Inferior Temporal Lobe	brain
21	chr7:102017200-102025000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr7:102017200-102028200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr7:102017200-102031000	Strong transcription	Fetal Intestine Small	intestine
24	chr7:102017200-102031200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr7:102017400-102023000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr7:102017400-102025000	Strong transcription	Adipose Nuclei	Adipose
27	chr7:102017400-102036200	Weak transcription	Right Atrium	heart
28	chr7:102017600-102023600	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr7:102017600-102025000	Strong transcription	Placenta	Placenta
30	chr7:102017600-102028200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr7:102017800-102023400	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr7:102018400-102035800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr7:102018600-102024000	Weak transcription	NHLF	lung
34	chr7:102018800-102023800	Weak transcription	Right Ventricle	heart
35	chr7:102018800-102023800	Weak transcription	Spleen	Spleen
36	chr7:102018800-102027200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr7:102018800-102031000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr7:102018800-102031000	Weak transcription	NHEK	skin
39	chr7:102018800-102031200	Weak transcription	Pancreas	Pancrea
40	chr7:102018800-102032800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr7:102018800-102036000	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr7:102018800-102036000	Weak transcription	Colonic Mucosa	Colon
43	chr7:102018800-102036200	Weak transcription	Esophagus	oesophagus
44	chr7:102019000-102024200	Weak transcription	Ovary	ovary
45	chr7:102019000-102036200	Weak transcription	Gastric	stomach
46	chr7:102020000-102026000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr7:102020200-102023000	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr7:102020200-102029200	Strong transcription	K562	blood
49	chr7:102020400-102023000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr7:102020400-102027400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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