Variant report

Variant	rs6975847
Chromosome Location	chr7:16793504-16793505
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:16792720..16796708-chr7:16843218..16846000,6	MCF-7	breast:
2	chr7:16685517..16687243-chr7:16793230..16795207,2	K562	blood:
3	chr7:16793468..16795066-chr7:16813077..16814664,2	MCF-7	breast:
4	chr15:52263919..52265515-chr7:16793247..16794965,2	MCF-7	breast:
5	chr7:16793269..16796429-chr7:16820580..16823340,4	MCF-7	breast:
6	chr7:16460318..16462710-chr7:16792580..16794734,3	K562	blood:
7	chr17:39676906..39679215-chr7:16792005..16794424,2	MCF-7	breast:
8	chr7:16684788..16686640-chr7:16792209..16794458,2	MCF-7	breast:
9	chr7:16735197..16737056-chr7:16793469..16795532,2	MCF-7	breast:
10	chr7:16776351..16778265-chr7:16793377..16796196,2	K562	blood:
11	chr7:16785410..16787895-chr7:16793449..16795182,2	MCF-7	breast:
12	chr7:16793297..16794819-chr7:16840473..16842534,2	MCF-7	breast:
13	chr7:16685077..16688645-chr7:16790567..16794834,4	K562	blood:
14	chr7:16793190..16795518-chr7:16923523..16926249,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000171346	Chromatin interaction
ENSG00000166477	Chromatin interaction
ENSG00000136261	Chromatin interaction
ENSG00000214960	Chromatin interaction
ENSG00000106541	Chromatin interaction
ENSG00000106524	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10233465	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10238328	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1149519	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1149522	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1149524	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1149526	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12530923	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[ASN][1000 genomes]
rs12535558	0.87[ASN][1000 genomes]
rs13244013	0.92[ASN][1000 genomes]
rs1997114	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1997115	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2085706	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290836	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2290837	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs34614062	0.87[ASN][1000 genomes]
rs3779051	0.82[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3807490	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3807492	0.89[CHB][hapmap];0.91[JPT][hapmap]
rs3807509	0.84[CHB][hapmap];0.91[CHD][hapmap];0.98[ASN][1000 genomes]
rs3823652	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4400279	0.87[ASN][1000 genomes]
rs4721535	0.99[ASN][1000 genomes]
rs4721536	0.98[ASN][1000 genomes]
rs4721538	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4721539	0.89[CHB][hapmap];0.91[JPT][hapmap]
rs55802535	0.84[ASN][1000 genomes]
rs62441050	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6461275	0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6942785	0.81[EUR][1000 genomes]
rs6951449	0.85[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap]
rs6962578	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	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs706055	0.99[ASN][1000 genomes]
rs73299615	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7781646	0.84[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7809197	1.00[ASN][1000 genomes]
rs818803	0.82[CEU][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs818804	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[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	nsv1016642	chr7:15884061-16799788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	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
3	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6975847	CNOT6	trans	parietal	SCAN
rs6975847	TWIST1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:16792600-16794200	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr7:16792800-16793600	Active TSS	Primary hematopoietic stem cells	blood
3	chr7:16792800-16793600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr7:16792800-16793600	Active TSS	Brain Germinal Matrix	brain
5	chr7:16792800-16793600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
6	chr7:16792800-16793600	Active TSS	Fetal Thymus	thymus
7	chr7:16792800-16793600	Active TSS	Thymus	Thymus
8	chr7:16792800-16794000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr7:16792800-16794000	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr7:16792800-16794000	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr7:16792800-16794000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
12	chr7:16792800-16794000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr7:16792800-16794000	Active TSS	Primary T cells from cord blood	blood
14	chr7:16792800-16794000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
15	chr7:16792800-16794000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr7:16792800-16794000	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr7:16792800-16794000	Active TSS	HMEC	breast
18	chr7:16792800-16794000	Active TSS	NHEK	skin
19	chr7:16792800-16794200	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr7:16792800-16794200	Active TSS	iPS-18 Cell Line	embryonic stem cell
21	chr7:16792800-16794200	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr7:16792800-16794200	Active TSS	A549	lung
23	chr7:16792800-16794200	Active TSS	K562	blood
24	chr7:16792800-16794400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr7:16792800-16794400	Active TSS	H1 Cell Line	embryonic stem cell
26	chr7:16792800-16794400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr7:16792800-16794400	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr7:16792800-16794400	Active TSS	Hela-S3	cervix
29	chr7:16792800-16794600	Active TSS	H9 Cell Line	embryonic stem cell
30	chr7:16792800-16794800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr7:16792800-16794800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr7:16792800-16794800	Active TSS	Duodenum Mucosa	Duodenum
33	chr7:16792800-16794800	Active TSS	Fetal Kidney	kidney
34	chr7:16792800-16795000	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr7:16792800-16795000	Active TSS	Brain Angular Gyrus	brain
36	chr7:16792800-16795000	Active TSS	Fetal Brain Male	brain
37	chr7:16792800-16795200	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr7:16792800-16795400	Active TSS	Right Atrium	heart
39	chr7:16792800-16795600	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr7:16792800-16796200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr7:16792800-16796400	Active TSS	Fetal Intestine Small	intestine
42	chr7:16792800-16796600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr7:16792800-16796600	Active TSS	Fetal Brain Female	brain
44	chr7:16793000-16793600	Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr7:16793000-16793600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
46	chr7:16793000-16793600	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
47	chr7:16793000-16793600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
48	chr7:16793000-16793600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr7:16793000-16793600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
50	chr7:16793000-16793600	Active TSS	Skeletal Muscle Male	skeletal muscle

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