Variant report

Variant	rs7645278
Chromosome Location	chr3:46974100-46974101
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46968433..46974874-chr3:46985986..46991697,10	MCF-7	breast:
2	chr3:46967009..46980239-chr3:47015804..47024437,23	MCF-7	breast:
3	chr3:46973841..46975600-chr3:47001098..47002983,2	MCF-7	breast:
4	chr3:46971685..46974752-chr3:47019618..47022746,3	MCF-7	breast:
5	chr3:46966739..46968792-chr3:46972024..46974475,2	K562	blood:
6	chr3:46971793..46974784-chr3:46975168..46977943,4	MCF-7	breast:
7	chr3:46965569..46968989-chr3:46970425..46974513,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160799	Chromatin interaction
ENSG00000160796	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1001284	0.92[ASN][1000 genomes]
rs10461018	0.83[ASW][hapmap];0.87[JPT][hapmap];0.93[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs1079276	0.81[JPT][hapmap]
rs10865943	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11130110	0.87[JPT][hapmap]
rs11130111	0.86[JPT][hapmap]
rs1138518	0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11705936	0.98[ASN][1000 genomes]
rs11719795	0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11720139	1.00[YRI][hapmap]
rs12491473	0.81[AFR][1000 genomes]
rs13061071	0.81[JPT][hapmap]
rs1463393	0.81[AFR][1000 genomes]
rs1466275	0.90[ASN][1000 genomes]
rs17784127	0.91[YRI][hapmap]
rs2061197	0.91[ASW][hapmap];0.87[JPT][hapmap];0.97[LWK][hapmap];0.83[MEX][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs2168443	0.91[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap]
rs2242116	0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];0.94[ASN][1000 genomes]
rs2278963	0.83[ASW][hapmap];0.91[YRI][hapmap]
rs2290545	0.83[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs2290546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2305634	0.81[JPT][hapmap]
rs2305635	0.90[YRI][hapmap]
rs2305638	0.81[JPT][hapmap]
rs4078466	0.81[JPT][hapmap]
rs4082155	0.81[JPT][hapmap]
rs4539969	0.90[ASN][1000 genomes]
rs4587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4682837	0.87[JPT][hapmap]
rs4682844	0.91[ASW][hapmap];0.87[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs4682845	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4683294	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs4683296	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683297	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683298	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4683299	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4683300	0.91[ASN][1000 genomes]
rs4683301	0.91[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs4683322	0.83[ASW][hapmap];0.91[YRI][hapmap]
rs62248439	0.81[AFR][1000 genomes]
rs6442038	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6442039	0.81[CEU][hapmap];0.90[ASN][1000 genomes]
rs6442040	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6767907	0.91[YRI][hapmap]
rs6780601	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs724448	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs724449	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs724450	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.94[ASN][1000 genomes]
rs7433300	0.83[ASW][hapmap];0.91[YRI][hapmap]
rs749512	0.83[ASW][hapmap];1.00[YRI][hapmap]
rs7623898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628747	0.87[JPT][hapmap]
rs7635480	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7646906	0.93[ASN][1000 genomes]
rs9311403	0.91[YRI][hapmap]
rs9852082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9855938	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	nsv460526	chr3:46935527-47001350	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	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
8	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7645278	SCAP	cis	cerebellum	SCAN
rs7645278	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs7645278	LZTFL1	cis	parietal	SCAN
rs7645278	CCDC12	cis	cerebellum	SCAN
rs7645278	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs7645278	SCAP	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46964600-46975600	Weak transcription	Fetal Brain Male	brain
2	chr3:46967400-46974600	Enhancers	HSMMtube	muscle
3	chr3:46967400-46975800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:46967400-46976000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:46967400-46976400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr3:46967400-46984400	Genic enhancers	Fetal Intestine Small	intestine
7	chr3:46967800-46976400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr3:46968000-46978800	Enhancers	Stomach Mucosa	stomach
9	chr3:46968400-46975800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:46968400-46976600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:46968400-46977600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:46968600-46975400	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr3:46969200-46976600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:46969200-46976600	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr3:46969400-46974400	Enhancers	Colonic Mucosa	Colon
16	chr3:46969400-46978400	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr3:46969600-46977400	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr3:46970200-46976800	Enhancers	Brain Hippocampus Middle	brain
19	chr3:46970200-46978600	Enhancers	Right Ventricle	heart
20	chr3:46970400-46976400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr3:46970400-46977600	Enhancers	Liver	Liver
22	chr3:46970400-46977800	Enhancers	Pancreas	Pancrea
23	chr3:46970600-46975000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr3:46970600-46975200	Enhancers	Primary hematopoietic stem cells	blood
25	chr3:46970600-46977600	Enhancers	Brain Angular Gyrus	brain
26	chr3:46970800-46974200	Enhancers	Aorta	Aorta
27	chr3:46970800-46975800	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr3:46970800-46976200	Enhancers	Spleen	Spleen
29	chr3:46970800-46977400	Enhancers	Placenta	Placenta
30	chr3:46970800-46977600	Enhancers	Left Ventricle	heart
31	chr3:46970800-46977600	Enhancers	Lung	lung
32	chr3:46970800-46977800	Enhancers	NHDF-Ad	bronchial
33	chr3:46970800-46979400	Enhancers	HUVEC	blood vessel
34	chr3:46970800-46984200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:46971000-46974200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:46971000-46975800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:46971000-46976000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:46971200-46975800	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr3:46971200-46976200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:46971200-46976800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:46971200-46988400	Strong transcription	Dnd41	blood
42	chr3:46971400-46977600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:46971600-46974600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:46971600-46975800	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr3:46971600-46976800	Enhancers	Fetal Lung	lung
46	chr3:46971600-46977400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr3:46971600-46977800	Enhancers	Esophagus	oesophagus
48	chr3:46971600-46978600	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr3:46971800-46974200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:46971800-46974200	Flanking Active TSS	Stomach Smooth Muscle	stomach

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