Variant report

Variant	rs144173
Chromosome Location	chr7:100416250-100416251
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:100415849-100416910	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr7:100415975-100416332	K562	blood:	n/a	n/a
3	POLR2A	chr7:100415772-100416464	K562	blood:	n/a	n/a
4	POLR2A	chr7:100416060-100416283	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr7:100415791-100416683	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr7:100416145-100416696	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:100289891..100291847-chr7:100416190..100417802,2	K562	blood:
2	chr7:100415072..100417547-chr7:100433376..100435074,2	K562	blood:
3	chr7:100411612..100416367-chr7:100416758..100421985,7	MCF-7	breast:
4	chr7:100414804..100417415-chr7:100464591..100466157,2	MCF-7	breast:

No data

Variant related genes	Relation type
EPHB4	TF binding region
ENSG00000196411	Chromatin interaction
ENSG00000263672	Chromatin interaction
ENSG00000087077	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs221804	0.82[EUR][1000 genomes]
rs2230585	0.96[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2247445	0.85[JPT][hapmap]
rs2250818	0.85[JPT][hapmap]
rs2406146	0.93[EUR][1000 genomes]
rs2472559	0.93[EUR][1000 genomes]
rs2571607	0.85[JPT][hapmap]
rs314309	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs314310	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs314319	0.86[ASN][1000 genomes]
rs314327	0.84[ASN][1000 genomes]
rs314341	0.87[EUR][1000 genomes]
rs314343	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs314344	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs314347	0.89[EUR][1000 genomes]
rs314353	1.00[CEU][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs314356	1.00[CEU][hapmap]
rs314357	0.97[EUR][1000 genomes]
rs314358	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.80[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs314359	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3847061	0.84[ASN][1000 genomes]
rs3857809	0.80[ASN][1000 genomes]
rs3890144	0.83[CHB][hapmap]
rs482308	0.84[CEU][hapmap]
rs489951	0.85[CEU][hapmap]
rs531503	0.85[CEU][hapmap]
rs539445	0.85[CEU][hapmap]
rs542137	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
2	nsv470381	chr7:100240191-100431980	Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1020837	chr7:100313122-100508635	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	nsv888796	chr7:100313420-100423365	Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	nsv464647	chr7:100374087-100497131	Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
9	nsv607965	chr7:100374087-100497131	Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
10	nsv1032673	chr7:100382250-100606794	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
11	nsv888797	chr7:100386900-100482026	Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
12	nsv888798	chr7:100406144-100472826	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
13	nsv888799	chr7:100406144-100497131	Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
14	nsv967435	chr7:100406273-100422961	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
15	nsv888800	chr7:100411278-100436446	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
16	nsv888801	chr7:100416250-100497131	Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs144173	VGF	cis	cerebellum	SCAN
rs144173	MCM7	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100399600-100422200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:100399600-100422200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
3	chr7:100399800-100422400	Strong transcription	H9 Cell Line	embryonic stem cell
4	chr7:100399800-100422400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr7:100400000-100422200	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr7:100400400-100422200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr7:100401600-100420800	Weak transcription	Brain Angular Gyrus	brain
8	chr7:100401600-100421800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr7:100401600-100421800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr7:100401600-100422000	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr7:100401600-100422000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr7:100401600-100422600	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr7:100401600-100423200	Weak transcription	Brain Anterior Caudate	brain
14	chr7:100401800-100416600	Weak transcription	Stomach Mucosa	stomach
15	chr7:100401800-100419600	Weak transcription	Right Atrium	heart
16	chr7:100401800-100421400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr7:100401800-100421400	Strong transcription	Fetal Stomach	stomach
18	chr7:100401800-100422200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr7:100401800-100422200	Weak transcription	Fetal Heart	heart
20	chr7:100401800-100422400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr7:100401800-100422400	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr7:100401800-100422400	Strong transcription	Fetal Intestine Large	intestine
23	chr7:100401800-100422600	Weak transcription	Fetal Brain Male	brain
24	chr7:100401800-100422600	Strong transcription	Fetal Intestine Small	intestine
25	chr7:100401800-100423000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr7:100402000-100421200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr7:100402000-100421800	Strong transcription	Fetal Muscle Trunk	muscle
28	chr7:100402000-100421800	Strong transcription	NHEK	skin
29	chr7:100402000-100422000	Strong transcription	Fetal Muscle Leg	muscle
30	chr7:100402000-100422600	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr7:100402000-100422600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr7:100402200-100418400	Strong transcription	Duodenum Mucosa	Duodenum
33	chr7:100402200-100418600	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr7:100402200-100421600	Strong transcription	Adipose Nuclei	Adipose
35	chr7:100402200-100421600	Strong transcription	Stomach Smooth Muscle	stomach
36	chr7:100402200-100421800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr7:100402400-100419000	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr7:100402400-100422000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr7:100402400-100422000	Strong transcription	Fetal Lung	lung
40	chr7:100402600-100421800	Strong transcription	Lung	lung
41	chr7:100403200-100416400	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr7:100403200-100420000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr7:100403200-100422000	Strong transcription	Placenta Amnion	Placenta Amnion
44	chr7:100403400-100422400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr7:100403600-100421800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr7:100405000-100420400	Strong transcription	HUVEC	blood vessel
47	chr7:100406600-100417600	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr7:100406800-100421200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr7:100407200-100420000	Strong transcription	Ovary	ovary
50	chr7:100407400-100416400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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