Variant report

Variant	rs6948536
Chromosome Location	chr7:100731829-100731830
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:100731671-100733078	K562	blood:	n/a	n/a
2	POLR2A	chr7:100731704-100732111	GM12891	blood:	n/a	n/a
3	POLR2A	chr7:100731651-100732049	K562	blood:	n/a	n/a
4	POLR2A	chr7:100731794-100731901	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr7:100731829-100731830	K562	blood:	n/a	n/a
6	POLR2A	chr7:100729856-100732041	GM12878	blood:	n/a	n/a
7	POLR2A	chr7:100731722-100731962	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr7:100730027-100733736	K562	blood:	n/a	n/a
9	POLR2A	chr7:100730371-100731931	GM12878	blood:	n/a	n/a
10	POLR2A	chr7:100729990-100733585	GM12892	blood:	n/a	n/a
11	POLR2A	chr7:100730888-100732451	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:100730465..100732139-chr7:100784272..100786414,2	MCF-7	breast:
2	chr7:100730490..100732421-chr7:100773109..100775504,2	K562	blood:
3	chr7:100724040..100726394-chr7:100730905..100732742,2	MCF-7	breast:
4	chr7:100730924..100734717-chr7:100859526..100862672,3	MCF-7	breast:
5	chr7:100485325..100486982-chr7:100730736..100732316,2	K562	blood:

No data

Variant related genes	Relation type
TRIM56	TF binding region
ENSG00000087087	Chromatin interaction
ENSG00000106400	Chromatin interaction
ENSG00000106397	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10953319	0.81[ASN][1000 genomes]
rs11761638	0.84[ASN][1000 genomes]
rs12535610	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12912	0.95[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13229117	0.92[ASN][1000 genomes]
rs34442394	0.84[AMR][1000 genomes]
rs36093166	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4292618	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4480033	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4524722	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4621721	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4727478	0.85[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4729661	0.82[MKK][hapmap]
rs62483743	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62483746	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6465783	0.95[CEU][hapmap];0.83[LWK][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6465785	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6945021	0.82[ASN][1000 genomes]
rs6945281	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6950982	0.84[ASW][hapmap];1.00[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap]
rs6956010	0.84[ASW][hapmap];1.00[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap]
rs6957750	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6965671	0.95[CEU][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs6966570	0.95[CEU][hapmap]
rs6968929	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs757722	1.00[YRI][hapmap]
rs7801428	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1832517	chr7:100355490-100749246	Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv2758125	chr7:100355490-100749246	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	esv2759547	chr7:100355490-100749246	Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	esv1826021	chr7:100525848-100749246	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv1846644	chr7:100525848-100749246	Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv1822460	chr7:100606044-100749246	Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv427796	chr7:100606044-100749246	Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv428181	chr7:100606044-100749246	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv831074	chr7:100606051-100745532	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv1031942	chr7:100606734-100788660	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
11	esv1833777	chr7:100632790-100800131	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
12	nsv1033081	chr7:100669629-100771824	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
13	nsv831075	chr7:100692297-100917018	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
14	nsv933653	chr7:100701931-101515782	Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
15	nsv1030604	chr7:100717732-101223465	Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6948536	FBXL13	cis	cerebellum	SCAN
rs6948536	MGC72080	cis	parietal	SCAN
rs6948536	TRIM4	cis	cerebellum	SCAN
rs6948536	Hs.397369	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100729400-100732200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr7:100729400-100734000	Weak transcription	Fetal Brain Female	brain
3	chr7:100729400-100736000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr7:100729400-100737800	Weak transcription	Small Intestine	intestine
5	chr7:100729400-100742600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr7:100729400-100742600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr7:100729400-100742800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr7:100729400-100742800	Weak transcription	Brain Substantia Nigra	brain
9	chr7:100729600-100732000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr7:100729600-100732600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr7:100729600-100734200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr7:100729600-100735000	Weak transcription	Fetal Kidney	kidney
13	chr7:100729600-100736600	Weak transcription	NH-A	brain
14	chr7:100729600-100742800	Weak transcription	Brain Angular Gyrus	brain
15	chr7:100729800-100733000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr7:100729800-100733400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr7:100729800-100734800	Genic enhancers	Primary T cells fromperipheralblood	blood
18	chr7:100730000-100733200	Genic enhancers	Right Ventricle	heart
19	chr7:100730000-100733400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr7:100730000-100733400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr7:100730000-100733400	Strong transcription	Osteobl	bone
22	chr7:100730000-100733800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:100730200-100732600	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr7:100730200-100733000	Genic enhancers	Placenta	Placenta
25	chr7:100730200-100733200	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr7:100730200-100733400	Genic enhancers	Spleen	Spleen
27	chr7:100730200-100733600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr7:100730200-100734600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr7:100730200-100734800	Strong transcription	Fetal Thymus	thymus
30	chr7:100730200-100735000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr7:100730200-100735200	Strong transcription	Fetal Muscle Trunk	muscle
32	chr7:100730200-100735400	Strong transcription	Fetal Stomach	stomach
33	chr7:100730400-100732200	Weak transcription	Right Atrium	heart
34	chr7:100730400-100732400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr7:100730400-100732600	Weak transcription	Fetal Lung	lung
36	chr7:100730400-100732600	Genic enhancers	Placenta Amnion	Placenta Amnion
37	chr7:100730400-100732800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr7:100730400-100733000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr7:100730400-100733000	Genic enhancers	Pancreas	Pancrea
40	chr7:100730400-100733200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
41	chr7:100730400-100733200	Genic enhancers	Stomach Smooth Muscle	stomach
42	chr7:100730400-100733400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr7:100730400-100733400	Strong transcription	Brain Hippocampus Middle	brain
44	chr7:100730400-100733600	Strong transcription	Aorta	Aorta
45	chr7:100730400-100733800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
46	chr7:100730400-100734000	Weak transcription	Primary B cells from cord blood	blood
47	chr7:100730400-100734200	Strong transcription	Fetal Intestine Small	intestine
48	chr7:100730400-100734600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr7:100730400-100734800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr7:100730400-100734800	Strong transcription	Primary T cells from cord blood	blood

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