Variant report

Variant	rs7628747
Chromosome Location	chr3:47001990-47001991
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:46988088..46989870-chr3:47001912..47004802,2	MCF-7	breast:
2	chr3:47000539..47004616-chr3:47005854..47010349,8	K562	blood:
3	chr3:47000442..47004800-chr3:47015859..47022252,7	K562	blood:
4	chr3:47000992..47003826-chr3:47019439..47023758,5	MCF-7	breast:
5	chr3:46979541..46981499-chr3:47001280..47002981,2	K562	blood:
6	chr3:47001947..47004283-chr3:47011185..47013637,2	MCF-7	breast:
7	chr3:46973841..46975600-chr3:47001098..47002983,2	MCF-7	breast:
8	chr3:46987457..46990723-chr3:46999774..47002993,3	MCF-7	breast:
9	chr3:46971047..46973675-chr3:47000415..47002568,2	MCF-7	breast:
10	chr3:46994661..46997196-chr3:47000542..47003538,2	MCF-7	breast:
11	chr3:47000243..47004408-chr3:47018008..47023852,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000160799	Chromatin interaction
ENSG00000160796	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10433549	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs10461018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1079276	0.96[CEU][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs1108301	0.96[EUR][1000 genomes]
rs11130110	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11130111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11130112	1.00[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11130115	1.00[ASW][hapmap];0.96[CEU][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.90[LWK][hapmap];0.88[MEX][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap]
rs1138518	0.82[JPT][hapmap]
rs11716553	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11719795	0.87[JPT][hapmap]
rs11720139	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs11917474	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12152493	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12491473	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12630534	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13061071	1.00[ASW][hapmap];0.96[CEU][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.90[LWK][hapmap];0.88[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap]
rs13062681	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13066214	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs13077398	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13091054	0.84[EUR][1000 genomes]
rs1463393	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17784127	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs1869869	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1869871	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2061197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2168443	0.82[JPT][hapmap]
rs2242116	0.82[JPT][hapmap];0.82[MEX][hapmap]
rs2278963	0.89[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs2290546	0.87[JPT][hapmap]
rs2305634	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs2305635	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs2305638	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs2385867	0.90[EUR][1000 genomes]
rs34103310	0.86[EUR][1000 genomes]
rs34344887	0.92[EUR][1000 genomes]
rs4078466	0.92[CEU][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs4082155	1.00[ASW][hapmap];0.92[CEU][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.82[EUR][1000 genomes]
rs4234465	1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4587	0.87[JPT][hapmap]
rs4682831	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4682837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4682844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4682852	0.96[CEU][hapmap]
rs4683296	0.82[JPT][hapmap]
rs4683297	0.87[JPT][hapmap]
rs4683298	0.86[JPT][hapmap]
rs4683301	0.81[YRI][hapmap]
rs4683322	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs55843455	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56217494	0.81[EUR][1000 genomes]
rs61729713	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62246375	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62248439	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6442040	0.87[JPT][hapmap]
rs66539935	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs66564457	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6763236	0.85[EUR][1000 genomes]
rs6767907	0.89[CEU][hapmap];0.91[TSI][hapmap]
rs6772670	0.95[CEU][hapmap]
rs6774733	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6794193	0.84[EUR][1000 genomes]
rs6808742	0.88[EUR][1000 genomes]
rs724448	0.81[JPT][hapmap];0.81[YRI][hapmap]
rs724449	0.82[JPT][hapmap];0.81[YRI][hapmap]
rs724450	0.82[JPT][hapmap]
rs749511	0.89[CEU][hapmap];0.80[GIH][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs749512	0.82[CEU][hapmap]
rs7610636	0.89[EUR][1000 genomes]
rs7617689	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7625067	0.86[EUR][1000 genomes]
rs7625070	0.86[EUR][1000 genomes]
rs7633698	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7636252	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7637302	0.83[EUR][1000 genomes]
rs7640397	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7645278	0.87[JPT][hapmap]
rs9311403	0.92[CEU][hapmap]
rs9837343	0.89[CEU][hapmap];0.91[TSI][hapmap]
rs9852082	0.86[JPT][hapmap]
rs9855938	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv915922	chr3:46768104-47009805	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv3800	chr3:46961648-47007241	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1012682	chr3:46973552-47016357	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
9	nsv1009396	chr3:46994991-47048166	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7628747	CCDC12	cis	cerebellum	SCAN
rs7628747	CCR1	cis	cerebellum	SCAN
rs7628747	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs7628747	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs7628747	SCAP	cis	parietal	SCAN
rs7628747	SCAP	cis	cerebellum	SCAN
rs7628747	PRKAR2A	cis	cerebellum	SCAN
rs7628747	HYAL2	cis	cerebellum	SCAN
rs7628747	C3orf75	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46985800-47004400	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr3:46988000-47003200	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr3:46990000-47006800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:46993400-47003600	Enhancers	Fetal Heart	heart
5	chr3:46993600-47003200	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr3:46994200-47002200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr3:46994200-47003200	Genic enhancers	Fetal Intestine Small	intestine
8	chr3:46995400-47002200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
9	chr3:46995400-47003200	Enhancers	Fetal Intestine Large	intestine
10	chr3:46995400-47003400	Enhancers	Primary hematopoietic stem cells	blood
11	chr3:46995600-47004200	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr3:46995800-47002400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr3:46995800-47003200	Enhancers	Primary B cells from cord blood	blood
14	chr3:46995800-47005200	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr3:46996000-47004200	Enhancers	Primary T cells from cord blood	blood
16	chr3:46996000-47004600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr3:46996000-47004800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr3:46996000-47007200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr3:46996400-47005000	Genic enhancers	Primary B cells from peripheral blood	blood
20	chr3:46996600-47002600	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr3:46996600-47003600	Enhancers	Stomach Mucosa	stomach
22	chr3:46998400-47002200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:46998400-47003200	Genic enhancers	Dnd41	blood
24	chr3:46998600-47003200	Enhancers	Rectal Smooth Muscle	rectum
25	chr3:46999000-47003400	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr3:46999200-47002400	Weak transcription	Aorta	Aorta
27	chr3:46999200-47003200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr3:46999200-47003600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:46999200-47004400	Enhancers	Liver	Liver
30	chr3:46999600-47002000	Weak transcription	A549	lung
31	chr3:46999600-47003600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:46999800-47002200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:46999800-47003200	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr3:46999800-47003200	Genic enhancers	Fetal Thymus	thymus
35	chr3:46999800-47003200	Enhancers	Ovary	ovary
36	chr3:46999800-47003200	Enhancers	Pancreas	Pancrea
37	chr3:46999800-47003400	Enhancers	Brain Substantia Nigra	brain
38	chr3:46999800-47004800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr3:47000000-47002000	Enhancers	Psoas Muscle	Psoas
40	chr3:47000000-47002000	Enhancers	Right Ventricle	heart
41	chr3:47000000-47002200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:47000000-47002400	Enhancers	Small Intestine	intestine
43	chr3:47000000-47002600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr3:47000000-47002600	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr3:47000000-47003000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr3:47000000-47003000	Enhancers	Placenta	Placenta
47	chr3:47000000-47003200	Enhancers	Brain Angular Gyrus	brain
48	chr3:47000000-47003200	Enhancers	Brain Hippocampus Middle	brain
49	chr3:47000000-47003200	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr3:47000000-47003200	Enhancers	Left Ventricle	heart

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