Variant report

Variant	rs6962578
Chromosome Location	chr7:16799832-16799833
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:16779818..16782062-chr7:16798409..16800212,3	K562	blood:
2	chr7:16798134..16800758-chr7:16806574..16808872,2	MCF-7	breast:
3	chr7:16793032..16794722-chr7:16798286..16800763,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000106537	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10233465	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10238328	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1149519	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1149522	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1149524	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1149526	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12530923	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12535558	0.85[ASN][1000 genomes]
rs13244013	0.87[ASN][1000 genomes]
rs1997114	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1997115	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2085706	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2290836	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs2290837	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs34614062	0.85[ASN][1000 genomes]
rs3779051	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3807490	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3807492	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs3807509	0.82[ASN][1000 genomes]
rs3823652	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4400279	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4721535	0.82[ASN][1000 genomes]
rs4721536	0.82[ASN][1000 genomes]
rs4721538	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4721539	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs55802535	1.00[ASN][1000 genomes]
rs62441050	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6461275	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6942785	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6951449	0.90[JPT][hapmap]
rs6975847	0.87[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6980298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs706055	0.82[ASN][1000 genomes]
rs73299615	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7781646	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7809197	0.84[ASN][1000 genomes]
rs818803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs818804	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028125	chr7:16529160-16847225	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1024059	chr7:16639432-16836425	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv824019	chr7:16794489-16800589	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	esv3475740	chr7:16794549-16800628	Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	esv3475741	chr7:16794549-16800658	Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	esv3475739	chr7:16794552-16800658	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:16795000-16800200	Weak transcription	Fetal Lung	lung
2	chr7:16795000-16804200	Weak transcription	HUVEC	blood vessel
3	chr7:16795000-16806000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr7:16795000-16810200	Weak transcription	HMEC	breast
5	chr7:16795000-16810400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr7:16795000-16828400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr7:16795200-16810000	Weak transcription	NHEK	skin
8	chr7:16795200-16810600	Weak transcription	Fetal Muscle Leg	muscle
9	chr7:16795400-16813000	Weak transcription	Right Ventricle	heart
10	chr7:16796000-16800400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr7:16796000-16801000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:16796200-16801800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr7:16796200-16804600	Weak transcription	Pancreas	Pancrea
14	chr7:16796200-16806400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr7:16796400-16810200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr7:16796600-16800200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr7:16796600-16800400	Weak transcription	Fetal Brain Female	brain
18	chr7:16796600-16801000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr7:16796600-16801800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr7:16796600-16803600	Weak transcription	Brain Anterior Caudate	brain
21	chr7:16796600-16804400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr7:16796600-16810400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr7:16796600-16816200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr7:16796800-16801800	Weak transcription	Fetal Heart	heart
25	chr7:16797200-16800400	Weak transcription	Fetal Intestine Large	intestine
26	chr7:16799000-16803200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr7:16799000-16807800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr7:16799000-16810400	Weak transcription	K562	blood
29	chr7:16799200-16800200	Weak transcription	Fetal Intestine Small	intestine
30	chr7:16799600-16800200	Enhancers	Primary B cells from cord blood	blood
31	chr7:16799600-16802600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr7:16799600-16810000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr7:16799600-16813000	Weak transcription	Stomach Mucosa	stomach
34	chr7:16799800-16800800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr7:16799800-16801800	Enhancers	Primary B cells from peripheral blood	blood
36	chr7:16799800-16801800	Weak transcription	Right Atrium	heart
37	chr7:16799800-16803000	Weak transcription	Gastric	stomach
38	chr7:16799800-16804600	Weak transcription	Left Ventricle	heart

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