Variant report

Variant	rs4728688
Chromosome Location	chr7:86832603-86832604
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	chr7:86831503-86832800	A549	lung:	n/a	n/a
2	POLR2A	chr7:86832202-86832695	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr7:86832200-86832681	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr7:86831404-86832986	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr7:86830832-86833049	HepG2	liver:	n/a	n/a
6	POLR2A	chr7:86832001-86832782	PFSK-1	brain:	n/a	n/a
7	POLR2A	chr7:86831390-86832741	GM12878	blood:	n/a	n/a
8	POLR2A	chr7:86827931-86832734	GM18505	blood:	n/a	n/a
9	POLR2A	chr7:86831480-86832668	GM12878	blood:	n/a	n/a
10	POLR2A	chr7:86827959-86834469	GM12891	blood:	n/a	n/a
11	POLR2A	chr7:86830793-86832726	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr7:86827917-86832918	GM12878	blood:	n/a	n/a
13	POLR2A	chr7:86827909-86833452	GM12878	blood:	n/a	n/a
14	POLR2A	chr7:86832581-86832621	Hela-S3	cervix:	n/a	n/a
15	MTA3	chr7:86831924-86832671	GM12878	blood:	n/a	n/a
16	POLR2A	chr7:86819363-86833788	K562	blood:	n/a	n/a
17	POLR2A	chr7:86828020-86833495	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:86828750..86830318-chr7:86830762..86833577,2	MCF-7	breast:

Variant related genes	Relation type
TMEM243	TF binding region
ENSG00000135185	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10245036	0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs10263920	0.83[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1058972	0.82[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1558050	0.80[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.83[ASN][1000 genomes]
rs2286267	0.83[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs3810883	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs4236504	0.83[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.83[ASN][1000 genomes]
rs4728685	0.83[ASN][1000 genomes]
rs4728690	0.80[ASW][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.86[ASN][1000 genomes]
rs6952842	0.82[ASN][1000 genomes]
rs6957785	0.80[ASW][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.92[YRI][hapmap];0.83[ASN][1000 genomes]
rs6964225	0.85[ASW][hapmap];0.97[LWK][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs6966613	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6978590	0.90[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs7776634	0.83[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs7793356	0.83[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7800541	0.83[CHB][hapmap];0.95[JPT][hapmap];0.82[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	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	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
5	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
6	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
7	nsv1026193	chr7:86790391-86856448	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv539003	chr7:86790391-86856448	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv888677	chr7:86802025-87781111	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
10	nsv464622	chr7:86832603-87541248	Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
11	nsv607725	chr7:86832603-87541248	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS 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	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4728688	C7orf23	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:86783000-86834000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:86789800-86833000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr7:86793400-86833400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr7:86821000-86847400	Weak transcription	Stomach Mucosa	stomach
5	chr7:86822200-86841800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr7:86823600-86834000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr7:86823600-86834000	Weak transcription	Esophagus	oesophagus
8	chr7:86823600-86834000	Weak transcription	Fetal Stomach	stomach
9	chr7:86825000-86833800	Weak transcription	Spleen	Spleen
10	chr7:86825000-86834000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr7:86825000-86834000	Weak transcription	Lung	lung
12	chr7:86825000-86840000	Weak transcription	Ovary	ovary
13	chr7:86825200-86834000	Weak transcription	Colonic Mucosa	Colon
14	chr7:86825600-86847400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr7:86825800-86843600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr7:86826000-86833200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr7:86826600-86833800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr7:86826600-86833800	Weak transcription	Fetal Brain Male	brain
19	chr7:86826600-86834000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr7:86826600-86834400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr7:86826600-86835000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr7:86826800-86833000	Weak transcription	NHEK	skin
23	chr7:86826800-86846000	Weak transcription	Fetal Kidney	kidney
24	chr7:86826800-86848200	Weak transcription	Left Ventricle	heart
25	chr7:86827000-86834000	Weak transcription	Hela-S3	cervix
26	chr7:86827800-86833800	Weak transcription	Placenta	Placenta
27	chr7:86828000-86833000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr7:86828400-86833400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
29	chr7:86828400-86848200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr7:86828600-86833200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr7:86828600-86834000	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr7:86828800-86833800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr7:86828800-86834000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr7:86829000-86837600	Weak transcription	Fetal Heart	heart
35	chr7:86829600-86832800	Genic enhancers	Primary T cells from cord blood	blood
36	chr7:86829600-86832800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr7:86829600-86833800	Weak transcription	Adipose Nuclei	Adipose
38	chr7:86829800-86833200	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr7:86829800-86834200	Weak transcription	Aorta	Aorta
40	chr7:86829800-86848000	Weak transcription	Right Ventricle	heart
41	chr7:86830000-86833600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr7:86830000-86833800	Weak transcription	Brain Germinal Matrix	brain
43	chr7:86830000-86834000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr7:86830000-86835000	Weak transcription	Fetal Lung	lung
45	chr7:86830000-86839800	Weak transcription	HSMMtube	muscle
46	chr7:86830200-86833200	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr7:86830400-86833800	Weak transcription	Thymus	Thymus
48	chr7:86830600-86833400	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr7:86830600-86833800	Weak transcription	NHDF-Ad	bronchial
50	chr7:86831000-86834000	Weak transcription	HUVEC	blood vessel

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