Variant report

Variant	rs1058972
Chromosome Location	chr7:86789426-86789427
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:86789251-86789438	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr7:86780291-86795664	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:86787322..86790184-chr7:86793047..86794551,2	MCF-7	breast:
2	chr7:86785961..86790922-chr7:86794752..86798878,5	MCF-7	breast:
3	chr7:86690033..86691580-chr7:86786714..86789542,2	K562	blood:
4	chr7:86540771..86562582-chr7:86776173..86789890,50	K562	blood:

Variant related genes	Relation type
DMTF1	TF binding region
ENSG00000164659	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1011952	0.97[EUR][1000 genomes]
rs1011953	0.98[EUR][1000 genomes]
rs10245036	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10263920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10273826	0.94[CEU][hapmap];0.82[CHB][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs1558050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1574795	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs2074757	0.85[GIH][hapmap]
rs2106955	0.98[EUR][1000 genomes]
rs2108272	0.85[GIH][hapmap]
rs2190424	0.82[GIH][hapmap]
rs2286267	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2286268	0.82[GIH][hapmap]
rs3747807	0.85[GIH][hapmap]
rs3789251	0.85[GIH][hapmap]
rs3810883	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4236504	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4728685	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4728686	0.85[GIH][hapmap]
rs4728688	0.82[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4728690	0.82[GIH][hapmap];0.95[JPT][hapmap]
rs6465099	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6465100	0.87[EUR][1000 genomes]
rs6942878	0.98[EUR][1000 genomes]
rs6952842	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6957785	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6966613	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6975175	0.87[EUR][1000 genomes]
rs6978590	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs757159	1.00[CEU][hapmap];0.84[JPT][hapmap];0.98[EUR][1000 genomes]
rs769156	1.00[CEU][hapmap];0.86[TSI][hapmap];0.94[EUR][1000 genomes]
rs7776634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7792031	0.81[CEU][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7793356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7800541	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7810647	0.85[GIH][hapmap]
rs7812191	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025277	chr7:86299224-87206007	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv538999	chr7:86299224-87206007	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv532147	chr7:86299225-87121975	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats 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 target site	85 gene(s)	inside rSNPs	diseases
4	nsv1015870	chr7:86490491-86802320	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
5	nsv539000	chr7:86490491-86802320	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
6	nsv527889	chr7:86496042-86832603	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv1016761	chr7:86758544-86914152	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
8	nsv888676	chr7:86781423-86858824	Active TSS Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1058972	C7orf23	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:86782600-86811400	Weak transcription	Spleen	Spleen
2	chr7:86782800-86798000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr7:86782800-86798400	Weak transcription	Gastric	stomach
4	chr7:86782800-86810800	Weak transcription	Esophagus	oesophagus
5	chr7:86782800-86811400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr7:86783000-86798000	Weak transcription	Lung	lung
7	chr7:86783000-86834000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr7:86783200-86792600	Weak transcription	Placenta	Placenta
9	chr7:86783200-86799600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:86783800-86792600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr7:86784000-86789600	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr7:86784000-86792600	Weak transcription	Left Ventricle	heart
13	chr7:86784000-86794200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr7:86784000-86796000	Weak transcription	Colonic Mucosa	Colon
15	chr7:86784200-86791400	Weak transcription	Fetal Muscle Leg	muscle
16	chr7:86784200-86792400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr7:86784200-86792400	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr7:86784200-86792800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr7:86784200-86796200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr7:86784400-86789600	Weak transcription	Fetal Thymus	thymus
21	chr7:86784600-86792600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr7:86784600-86792600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr7:86784600-86792600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr7:86784600-86792800	Weak transcription	Thymus	Thymus
25	chr7:86784600-86793600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr7:86784600-86794800	Weak transcription	HSMMtube	muscle
27	chr7:86784600-86799600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr7:86784800-86792800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr7:86784800-86792800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr7:86785000-86791400	Weak transcription	Fetal Stomach	stomach
31	chr7:86785000-86792400	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr7:86785000-86795800	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr7:86785400-86792000	Weak transcription	Primary hematopoietic stem cells	blood
34	chr7:86785600-86792600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr7:86785600-86794200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr7:86785600-86813400	Weak transcription	Stomach Mucosa	stomach
37	chr7:86785600-86822600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr7:86785800-86789800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr7:86785800-86794200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr7:86786000-86789800	Weak transcription	Liver	Liver
41	chr7:86786000-86791400	Weak transcription	Primary B cells from peripheral blood	blood
42	chr7:86786000-86791400	Weak transcription	Small Intestine	intestine
43	chr7:86786000-86792600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr7:86786000-86792600	Weak transcription	Fetal Kidney	kidney
45	chr7:86786000-86792600	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr7:86786000-86792800	Weak transcription	Fetal Intestine Large	intestine
47	chr7:86786000-86795000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr7:86786000-86795200	Weak transcription	Aorta	Aorta
49	chr7:86786000-86795400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr7:86786000-86795400	Weak transcription	Psoas Muscle	Psoas

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