Variant report

Variant	rs6446272
Chromosome Location	chr3:49463287-49463288
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49460720..49464051-chr3:49464777..49467713,3	MCF-7	breast:
2	chr3:49463180..49464811-chr3:49464830..49467753,3	K562	blood:
3	chr3:49448910..49451821-chr3:49459047..49464749,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000067560	Chromatin interaction
ENSG00000145029	Chromatin interaction
ENSG00000145022	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10212296	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1050088	0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs1050450	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10640	0.94[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865955	0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs11130192	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11130193	0.83[ASN][1000 genomes]
rs11130196	0.82[ASN][1000 genomes]
rs11130199	0.86[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs11706370	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711485	0.89[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11711536	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11712569	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11713474	0.83[AMR][1000 genomes]
rs11715915	0.94[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716974	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11719996	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11720264	1.00[JPT][hapmap]
rs11919311	0.88[GIH][hapmap];0.86[JPT][hapmap]
rs11922013	0.91[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11926781	0.82[AMR][1000 genomes]
rs12330269	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12489092	1.00[JPT][hapmap]
rs13078949	0.85[GIH][hapmap]
rs13079082	0.88[AMR][1000 genomes]
rs13079643	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13086611	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13087851	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13090388	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1464566	0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1464567	0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1464568	0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1568661	0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs17080528	1.00[ASW][hapmap];0.94[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17650792	0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs1800668	0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1801143	1.00[ASW][hapmap];0.94[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.88[AMR][1000 genomes]
rs1987628	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34196454	0.86[AMR][1000 genomes]
rs34293138	0.86[AMR][1000 genomes]
rs34363169	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34427167	0.82[AMR][1000 genomes]
rs34588335	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34937635	0.87[ASN][1000 genomes]
rs35115732	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35169793	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35261698	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35701831	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs35999162	0.80[AMR][1000 genomes]
rs3811697	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes]
rs3811699	1.00[ASW][hapmap];0.94[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3870338	0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs3924462	0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs3926569	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4459909	0.94[ASN][1000 genomes]
rs4625	1.00[ASW][hapmap];0.94[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.88[AMR][1000 genomes]
rs4855839	0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs4855842	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4855843	0.83[ASN][1000 genomes]
rs4855852	0.88[GIH][hapmap];0.86[JPT][hapmap]
rs4855859	0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs4855864	0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs4855873	0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4855877	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs55957735	0.92[ASN][1000 genomes]
rs6446264	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6446274	0.87[ASN][1000 genomes]
rs6446277	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67216675	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67485053	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6766131	1.00[ASW][hapmap];0.94[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6766581	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6779524	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782577	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs6784820	0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6792911	0.86[ASN][1000 genomes]
rs6793308	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6797664	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6809216	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6997	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71324962	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7622302	0.94[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7623659	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7630869	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7633271	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7637999	0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs7643586	0.86[ASN][1000 genomes]
rs7646366	0.94[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7648841	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs885592	0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs9811982	0.94[CEU][hapmap]
rs9814873	0.94[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9818590	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9821311	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9827021	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9827708	0.94[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.87[TSI][hapmap]
rs9837027	1.00[ASW][hapmap];0.94[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes]
rs9841110	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9850072	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9853683	0.94[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9858280	1.00[ASW][hapmap];0.94[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes]
rs9858418	0.88[AMR][1000 genomes]
rs9859556	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9871380	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875617	0.94[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap]
rs9878943	0.84[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv963482	chr3:49459177-49486938	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs6446272	RBM6	cis	cerebellum	SCAN
rs6446272	AMT	cis	parietal	SCAN
rs6446272	NICN1	cis	cerebellum	SCAN
rs6446272	ZNF589	cis	parietal	SCAN
rs6446272	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs6446272	FAM212A	cis	Muscle Skeletal	GTEx
rs6446272	CISH	cis	parietal	SCAN
rs6446272	GPX1	cis	parietal	SCAN
rs6446272	NBEAL2	cis	cerebellum	SCAN
rs6446272	PARP3	cis	parietal	SCAN
rs6446272	IP6K2	cis	cerebellum	SCAN
rs6446272	KDM5B	trans	lymphoblastoid	seeQTL
rs6446272	RNF123	cis	cerebellum	SCAN
rs6446272	IHPK2	Cis_1M	lymphoblastoid	RTeQTL
rs6446272	RNF123	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49451200-49466200	Weak transcription	Psoas Muscle	Psoas
2	chr3:49455600-49466200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr3:49455800-49463800	Strong transcription	Dnd41	blood
4	chr3:49457400-49466000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:49457600-49465400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr3:49459200-49466200	Weak transcription	HUVEC	blood vessel
7	chr3:49459400-49465800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr3:49459600-49465200	Weak transcription	Hela-S3	cervix
9	chr3:49459600-49465600	Weak transcription	NHDF-Ad	bronchial
10	chr3:49459600-49466200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:49459600-49466200	Weak transcription	HMEC	breast
12	chr3:49459800-49465600	Weak transcription	NHEK	skin
13	chr3:49460200-49463600	Strong transcription	Brain Germinal Matrix	brain
14	chr3:49460200-49463800	Strong transcription	Lung	lung
15	chr3:49460200-49466000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr3:49460400-49463800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:49460400-49463800	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr3:49460400-49463800	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr3:49460400-49464000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:49460400-49464400	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr3:49460400-49464400	Strong transcription	Thymus	Thymus
22	chr3:49460400-49465800	Weak transcription	Brain Angular Gyrus	brain
23	chr3:49460400-49465800	Weak transcription	Right Atrium	heart
24	chr3:49460400-49466200	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr3:49460600-49463600	Strong transcription	Spleen	Spleen
26	chr3:49460600-49463800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:49460600-49464600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:49460600-49465600	Weak transcription	Esophagus	oesophagus
29	chr3:49460600-49465600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr3:49460600-49465600	Weak transcription	A549	lung
31	chr3:49460600-49465800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr3:49460600-49465800	Weak transcription	Brain Substantia Nigra	brain
33	chr3:49460600-49465800	Weak transcription	Fetal Brain Male	brain
34	chr3:49460600-49466000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr3:49460600-49466000	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr3:49460600-49466000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:49460600-49466000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr3:49460600-49466200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:49460600-49466200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:49460600-49466200	Weak transcription	Small Intestine	intestine
41	chr3:49460600-49466200	Weak transcription	Stomach Mucosa	stomach
42	chr3:49460600-49466200	Weak transcription	HSMM	muscle
43	chr3:49460600-49466200	Weak transcription	Osteobl	bone
44	chr3:49460800-49463800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr3:49460800-49464000	Strong transcription	Fetal Thymus	thymus
46	chr3:49460800-49465000	Strong transcription	Fetal Stomach	stomach
47	chr3:49460800-49465600	Weak transcription	NH-A	brain
48	chr3:49460800-49465800	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr3:49460800-49466000	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr3:49460800-49466000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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