Variant report

Variant	rs11970648
Chromosome Location	chr6:56627595-56627596
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56592975..56595181-chr6:56623797..56627807,3	MCF-7	breast:
2	chr6:56626571..56629083-chr6:56715214..56716823,2	MCF-7	breast:
3	chr6:56622975..56624888-chr6:56627094..56628814,2	K562	blood:
4	chr6:56624772..56628939-chr6:56706585..56709491,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231441	Chromatin interaction
ENSG00000151914	Chromatin interaction

Extended variants
information (count: 146 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs1024196	1.00[CHD][hapmap]
rs10498812	1.00[CEU][hapmap]
rs10498813	1.00[CEU][hapmap]
rs11756551	0.87[EUR][1000 genomes]
rs11961141	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11961342	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11968575	0.94[ASW][hapmap];0.81[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13190784	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[MEX][hapmap]
rs13191826	0.82[AMR][1000 genomes]
rs13192478	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13192567	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13194625	1.00[CEU][hapmap]
rs13194904	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs13198204	0.80[EUR][1000 genomes]
rs13198399	0.89[EUR][1000 genomes]
rs13198597	0.94[CEU][hapmap]
rs13198938	0.89[EUR][1000 genomes]
rs13200166	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs13200559	0.88[EUR][1000 genomes]
rs13200768	0.85[EUR][1000 genomes]
rs13200868	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13201639	0.80[EUR][1000 genomes]
rs13201733	0.80[EUR][1000 genomes]
rs13203000	0.81[CEU][hapmap];0.90[EUR][1000 genomes]
rs13203327	0.82[EUR][1000 genomes]
rs13203681	1.00[CEU][hapmap]
rs13204466	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs13205667	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs13207768	1.00[CEU][hapmap]
rs13208409	0.92[EUR][1000 genomes]
rs13210876	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13213878	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13215883	0.94[CEU][hapmap]
rs13217390	0.81[CEU][hapmap];0.90[EUR][1000 genomes]
rs13218913	1.00[CEU][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs13219546	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13219942	0.87[EUR][1000 genomes]
rs13220618	1.00[CEU][hapmap]
rs13220628	1.00[CEU][hapmap]
rs13220851	0.82[EUR][1000 genomes]
rs16888135	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16888171	1.00[CEU][hapmap];1.00[CHD][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs16888186	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs17684730	0.80[EUR][1000 genomes]
rs17684748	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs17684772	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs17684784	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs17684802	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs17684878	1.00[CEU][hapmap];0.81[MEX][hapmap]
rs17684884	1.00[CEU][hapmap]
rs17751682	0.81[MEX][hapmap]
rs17751695	0.81[MEX][hapmap]
rs17751966	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs17751977	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs17752046	1.00[CEU][hapmap]
rs17752106	1.00[CEU][hapmap]
rs1903332	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[MEX][hapmap]
rs2967960	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2967963	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3002003	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3002004	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3002006	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3002007	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3002008	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3002009	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3002010	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3002011	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34228698	0.83[EUR][1000 genomes]
rs34429594	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34455199	0.90[EUR][1000 genomes]
rs34463732	0.84[EUR][1000 genomes]
rs34465210	0.90[EUR][1000 genomes]
rs34500949	0.87[EUR][1000 genomes]
rs34566275	0.90[EUR][1000 genomes]
rs34587484	0.90[EUR][1000 genomes]
rs34612783	0.85[EUR][1000 genomes]
rs34623351	0.90[EUR][1000 genomes]
rs34703847	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34803237	0.90[EUR][1000 genomes]
rs34812826	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34824960	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34832779	0.89[EUR][1000 genomes]
rs34966024	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35089136	0.89[ASN][1000 genomes]
rs35326806	0.87[EUR][1000 genomes]
rs35494794	0.87[EUR][1000 genomes]
rs35566812	0.84[EUR][1000 genomes]
rs35609883	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35642890	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35696739	0.80[EUR][1000 genomes]
rs35873865	0.84[EUR][1000 genomes]
rs35876418	0.90[EUR][1000 genomes]
rs35886823	0.84[AMR][1000 genomes]
rs35920751	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35986172	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs36037734	0.80[EUR][1000 genomes]
rs36068365	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4074101	0.81[MEX][hapmap]
rs41267675	0.90[EUR][1000 genomes]
rs4275049	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4299824	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs4348308	1.00[CEU][hapmap]
rs4371846	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs4415160	1.00[CEU][hapmap]
rs4457154	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs4574644	0.89[ASN][1000 genomes]
rs4587171	0.83[CEU][hapmap];0.84[TSI][hapmap]
rs4640889	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56094263	0.89[ASN][1000 genomes]
rs56368885	0.87[EUR][1000 genomes]
rs58980183	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59085778	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59162324	0.89[ASN][1000 genomes]
rs59247267	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59432342	0.83[EUR][1000 genomes]
rs60498201	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61601344	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62411366	0.88[EUR][1000 genomes]
rs62411367	0.88[EUR][1000 genomes]
rs62411372	0.85[EUR][1000 genomes]
rs62411375	0.82[EUR][1000 genomes]
rs62411376	0.83[EUR][1000 genomes]
rs62412544	0.81[EUR][1000 genomes]
rs62412556	0.88[EUR][1000 genomes]
rs6904535	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6905603	1.00[CEU][hapmap]
rs6918949	1.00[CEU][hapmap];0.81[MEX][hapmap]
rs6926134	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6928104	0.86[EUR][1000 genomes]
rs6934714	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6938003	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71564854	0.83[EUR][1000 genomes]
rs71564856	0.80[EUR][1000 genomes]
rs71564861	0.80[EUR][1000 genomes]
rs7749100	1.00[CHD][hapmap]
rs7758867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[MEX][hapmap]
rs7760542	1.00[CHD][hapmap]
rs7761501	1.00[CEU][hapmap]
rs7761729	1.00[CEU][hapmap];0.81[MEX][hapmap]
rs7771085	1.00[CEU][hapmap]
rs7775134	1.00[CHD][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	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11970648	BMP5	cis	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56619800-56629200	Weak transcription	Pancreas	Pancrea
2	chr6:56621400-56629000	Weak transcription	Aorta	Aorta
3	chr6:56621400-56634200	Weak transcription	Spleen	Spleen
4	chr6:56622400-56637600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:56622800-56627800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr6:56622800-56628800	Weak transcription	Ovary	ovary
7	chr6:56622800-56631000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:56623000-56631000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr6:56623200-56628200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:56623200-56628800	Weak transcription	HepG2	liver
11	chr6:56623200-56629000	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr6:56623200-56629000	Weak transcription	HUVEC	blood vessel
13	chr6:56623200-56629200	Weak transcription	Stomach Mucosa	stomach
14	chr6:56623200-56631000	Weak transcription	Fetal Lung	lung
15	chr6:56623400-56628600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr6:56623600-56628600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr6:56623600-56631000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr6:56623600-56637200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr6:56623600-56637600	Weak transcription	Fetal Muscle Leg	muscle
20	chr6:56623800-56628400	Weak transcription	Right Atrium	heart
21	chr6:56623800-56628600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr6:56623800-56628800	Weak transcription	Lung	lung
23	chr6:56623800-56628800	Weak transcription	NH-A	brain
24	chr6:56623800-56630200	Weak transcription	HSMMtube	muscle
25	chr6:56623800-56630400	Weak transcription	Fetal Stomach	stomach
26	chr6:56624000-56628200	Weak transcription	Left Ventricle	heart
27	chr6:56624000-56628600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:56624000-56628600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr6:56624200-56628200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr6:56624200-56628800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:56624200-56628800	Weak transcription	Fetal Thymus	thymus
32	chr6:56624600-56628400	Weak transcription	Psoas Muscle	Psoas
33	chr6:56624600-56628600	Weak transcription	NHLF	lung
34	chr6:56624800-56628600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr6:56624800-56628600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr6:56624800-56628800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr6:56624800-56628800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr6:56624800-56628800	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr6:56624800-56628800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr6:56624800-56629000	Weak transcription	Brain Angular Gyrus	brain
41	chr6:56624800-56629000	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr6:56625000-56628600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr6:56625200-56628600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr6:56625200-56637800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr6:56625400-56629000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr6:56625400-56629000	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr6:56625400-56631400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr6:56625600-56628800	Weak transcription	Rectal Smooth Muscle	rectum
49	chr6:56625600-56637000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr6:56625600-56649800	Weak transcription	Brain Germinal Matrix	brain

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