Variant report

Variant	rs7628207
Chromosome Location	chr3:49754970-49754971
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:31)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:31 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49754469-49762505	GM12892	blood:	n/a	n/a
2	POLR2A	chr3:49752450-49757371	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:49754947-49755410	U87	brain:	n/a	n/a
4	POLR2A	chr3:49754970-49763587	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:49754889-49755763	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr3:49754901-49755281	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr3:49754039-49757529	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr3:49754800-49756322	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr3:49751816-49757616	U87	brain:	n/a	n/a
10	POLR2A	chr3:49752889-49762689	GM12892	blood:	n/a	n/a
11	POLR2A	chr3:49752911-49757637	HL-60	blood:	n/a	n/a
12	POLR2A	chr3:49754910-49755206	K562	blood:	n/a	n/a
13	POLR2A	chr3:49752081-49757341	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr3:49754271-49762558	U87	brain:	n/a	n/a
15	POLR2A	chr3:49754554-49762400	K562	blood:	n/a	n/a
16	POLR2A	chr3:49753358-49757465	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr3:49754956-49755249	GM12878	blood:	n/a	n/a
18	POLR2A	chr3:49754306-49757479	GM12892	blood:	n/a	n/a
19	POLR2A	chr3:49752820-49757544	GM12891	blood:	n/a	n/a
20	POLR2A	chr3:49754833-49757597	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr3:49754384-49762352	GM12891	blood:	n/a	n/a
22	POLR2A	chr3:49754930-49757529	HL-60	blood:	n/a	n/a
23	POLR2A	chr3:49752922-49755283	HepG2	liver:	n/a	n/a
24	POLR2A	chr3:49754229-49757561	GM12878	blood:	n/a	n/a
25	POLR2A	chr3:49752283-49757359	GM12878	blood:	n/a	n/a
26	POLR2A	chr3:49752258-49757457	K562	blood:	n/a	n/a
27	POLR2A	chr3:49754344-49755223	GM19193	blood:	n/a	n/a
28	POLR2A	chr3:49754947-49755326	U87	brain:	n/a	n/a
29	POLR2A	chr3:49754867-49756542	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr3:49753024-49764559	K562	blood:	n/a	n/a
31	POLR2A	chr3:49754940-49757534	GM12891	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:17936495..17938188-chr3:49752423..49755121,2	MCF-7	breast:
2	chr3:49735446..49741255-chr3:49749875..49755830,7	K562	blood:

No data

Variant related genes	Relation type
RNF123	TF binding region
ENSG00000164068	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10452032	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs1078341	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs10865956	1.00[CHD][hapmap]
rs11130208	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap]
rs11130211	0.94[CEU][hapmap]
rs11130217	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11709734	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11720705	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12583	1.00[CHD][hapmap]
rs12637313	0.88[CEU][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap]
rs12715437	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13317088	1.00[JPT][hapmap]
rs13322887	1.00[CHD][hapmap]
rs1352889	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs1491983	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs1491985	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1532204	0.94[CEU][hapmap]
rs1586827	1.00[CEU][hapmap]
rs1799844	0.89[EUR][1000 genomes]
rs1982861	1.00[CHD][hapmap]
rs1996663	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1996664	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2029591	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs2131108	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs2312462	1.00[CHD][hapmap]
rs2329021	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs28535523	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3020779	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs34890793	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap]
rs35129566	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4241405	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs4241407	1.00[CHD][hapmap]
rs4855833	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs4855845	1.00[CEU][hapmap]
rs4855846	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs4855882	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4855885	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs55997059	0.89[EUR][1000 genomes]
rs58339610	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59357103	0.87[EUR][1000 genomes]
rs59684465	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61557789	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62260663	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62260720	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62260723	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62262722	0.94[EUR][1000 genomes]
rs62262730	0.91[EUR][1000 genomes]
rs6446285	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs6774202	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs6790568	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6797299	0.94[CEU][hapmap]
rs6804970	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6809879	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7613603	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7620848	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7621797	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7637711	1.00[CEU][hapmap];1.00[CHD][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7649428	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9824435	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs9829155	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9830730	1.00[CEU][hapmap]
rs9835157	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9836756	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9849038	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9851651	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9862534	1.00[CHD][hapmap]
rs9870755	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9870858	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9883000	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription 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	90 gene(s)	inside rSNPs	diseases
3	esv1825898	chr3:49688948-49764849	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers 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 target site	53 gene(s)	inside rSNPs	diseases
4	esv1796605	chr3:49744556-49760567	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv482082	chr3:49754965-49757123	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs7628207	DALRD3	cis	parietal	SCAN
rs7628207	AMT	cis	Thyroid	GTEx
rs7628207	P4HTM	cis	parietal	SCAN
rs7628207	AMT	cis	parietal	SCAN
rs7628207	GNL3	cis	cerebellum	SCAN
rs7628207	OR9G4	trans	parietal	SCAN
rs7628207	RNF123	cis	parietal	SCAN
rs7628207	RNF123	cis	Artery Tibial	GTEx
rs7628207	ZNF589	cis	parietal	SCAN
rs7628207	GMPPB	cis	parietal	SCAN
rs7628207	WDR6	cis	cerebellum	SCAN
rs7628207	DALRD3	cis	cerebellum	SCAN
rs7628207	ITIH3	cis	cerebellum	SCAN
rs7628207	RBM6	cis	cerebellum	SCAN
rs7628207	AMT	cis	lung	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49728400-49756600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:49729200-49755800	Weak transcription	Right Atrium	heart
3	chr3:49732200-49755000	Strong transcription	Fetal Intestine Small	intestine
4	chr3:49734400-49756000	Strong transcription	Liver	Liver
5	chr3:49735400-49755400	Weak transcription	Stomach Mucosa	stomach
6	chr3:49736800-49756400	Weak transcription	HSMM	muscle
7	chr3:49739000-49756400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr3:49740000-49755600	Weak transcription	Fetal Brain Male	brain
9	chr3:49740200-49756000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr3:49740200-49756600	Weak transcription	HSMMtube	muscle
11	chr3:49740400-49755000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:49740600-49759800	Weak transcription	Hela-S3	cervix
13	chr3:49740800-49756400	Weak transcription	Osteobl	bone
14	chr3:49741400-49755200	Strong transcription	Placenta	Placenta
15	chr3:49741800-49755600	Weak transcription	HUVEC	blood vessel
16	chr3:49742600-49756200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:49743000-49756400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:49743000-49756800	Weak transcription	Small Intestine	intestine
19	chr3:49743400-49756200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:49743800-49755800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr3:49744000-49755400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr3:49744000-49756400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:49745000-49756000	Weak transcription	Primary B cells from cord blood	blood
24	chr3:49745200-49756000	Weak transcription	NH-A	brain
25	chr3:49745200-49756200	Weak transcription	Left Ventricle	heart
26	chr3:49745400-49756200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:49746400-49756600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:49747400-49755000	Strong transcription	Fetal Stomach	stomach
29	chr3:49748600-49755600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:49748800-49755400	Strong transcription	Fetal Intestine Large	intestine
31	chr3:49749400-49756600	Weak transcription	A549	lung
32	chr3:49749600-49755600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr3:49749800-49755000	Strong transcription	Gastric	stomach
34	chr3:49749800-49756400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
35	chr3:49750200-49755200	Strong transcription	Brain Inferior Temporal Lobe	brain
36	chr3:49750200-49755800	Strong transcription	Brain Cingulate Gyrus	brain
37	chr3:49750400-49755800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
38	chr3:49750800-49755800	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr3:49750800-49756000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr3:49751000-49756000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr3:49751000-49756000	Weak transcription	Psoas Muscle	Psoas
42	chr3:49751200-49755400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:49751200-49755600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr3:49751200-49755800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr3:49751200-49755800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr3:49751200-49756000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr3:49751200-49756200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr3:49751400-49755400	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr3:49751400-49756400	Strong transcription	NHLF	lung
50	chr3:49751600-49756000	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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