Variant report

Variant	rs6546829
Chromosome Location	chr2:73613789-73613790
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:73497659..73500414-chr2:73612511..73614881,2	MCF-7	breast:
2	chr2:73613233..73615069-chr2:73661651..73663882,2	MCF-7	breast:
3	chr2:73596191..73598481-chr2:73612504..73614239,2	K562	blood:
4	chr2:73460084..73462978-chr2:73611729..73614401,3	K562	blood:
5	chr2:73612210..73615081-chr2:73714696..73716979,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000221087	Chromatin interaction
ENSG00000163013	Chromatin interaction
ENSG00000214484	Chromatin interaction
ENSG00000135624	Chromatin interaction
ENSG00000135617	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10165862	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10175529	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10190002	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs1083922	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs10865398	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs11126395	0.81[ASN][1000 genomes]
rs11126396	0.81[ASN][1000 genomes]
rs11126399	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11693531	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11898362	0.81[ASN][1000 genomes]
rs12465867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1403412	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1406105	0.91[CHB][hapmap]
rs1522926	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1851546	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1852644	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1852647	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs1881246	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs1881247	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2017116	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs2037814	1.00[CHB][hapmap]
rs2091022	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2421489	0.91[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap]
rs2421545	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs2421546	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2901437	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35885918	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3820700	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs6546824	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6546826	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6546827	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6546832	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs6706235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6706409	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6710659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6716776	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6728128	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6747145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6748040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6749680	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs7560272	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7567017	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7567343	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7573275	0.82[ASN][1000 genomes]
rs7574291	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs7576824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7598901	0.92[CHB][hapmap]
rs7604588	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs780390	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs780396	1.00[CHB][hapmap];0.81[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv2778	chr2:73596272-73615138	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6546829	TPRKB	Cis_1M	lymphoblastoid	RTeQTL
rs6546829	ALMS1P	cis	Whole Blood	GTEx
rs6546829	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs6546829	ALMS1P	cis	Skin Sun Exposed Lower leg	GTEx
rs6546829	ALMS1	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73612000-73614000	Active TSS	Colonic Mucosa	Colon
2	chr2:73612000-73614200	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr2:73612000-73614200	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr2:73612000-73614200	Active TSS	NHDF-Ad	bronchial
5	chr2:73612000-73614600	Active TSS	H1 Cell Line	embryonic stem cell
6	chr2:73612000-73615000	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr2:73612000-73615200	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr2:73612200-73613800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:73612200-73613800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:73612200-73613800	Active TSS	Brain Cingulate Gyrus	brain
11	chr2:73612200-73613800	Active TSS	Colon Smooth Muscle	Colon
12	chr2:73612200-73613800	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr2:73612200-73613800	Active TSS	Fetal Thymus	thymus
14	chr2:73612200-73614000	Active TSS	Fetal Brain Male	brain
15	chr2:73612200-73614000	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr2:73612200-73614000	Active TSS	Psoas Muscle	Psoas
17	chr2:73612200-73614200	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr2:73612200-73614200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:73612200-73614200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:73612200-73614200	Active TSS	Fetal Kidney	kidney
21	chr2:73612200-73614200	Active TSS	Fetal Muscle Trunk	muscle
22	chr2:73612200-73614200	Active TSS	HSMM	muscle
23	chr2:73612200-73614200	Active TSS	NHLF	lung
24	chr2:73612200-73614400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr2:73612200-73614400	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr2:73612200-73614400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:73612200-73614400	Active TSS	Right Ventricle	heart
28	chr2:73612200-73614400	Active TSS	HSMMtube	muscle
29	chr2:73612200-73614600	Active TSS	GM12878-XiMat	blood
30	chr2:73612200-73614800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:73612400-73613800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:73612400-73613800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr2:73612400-73613800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:73612400-73613800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:73612400-73613800	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr2:73612400-73613800	Active TSS	Fetal Heart	heart
37	chr2:73612400-73613800	Active TSS	Stomach Mucosa	stomach
38	chr2:73612400-73613800	Active TSS	NH-A	brain
39	chr2:73612400-73613800	Active TSS	NHEK	skin
40	chr2:73612400-73614000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr2:73612400-73614000	Active TSS	Aorta	Aorta
42	chr2:73612400-73614000	Active TSS	Brain Substantia Nigra	brain
43	chr2:73612400-73614000	Active TSS	Esophagus	oesophagus
44	chr2:73612400-73614000	Active TSS	Gastric	stomach
45	chr2:73612400-73614000	Active TSS	Left Ventricle	heart
46	chr2:73612400-73614000	Active TSS	Lung	lung
47	chr2:73612400-73614000	Active TSS	Pancreas	Pancrea
48	chr2:73612400-73614000	Active TSS	Sigmoid Colon	Sigmoid Colon
49	chr2:73612400-73614000	Active TSS	Small Intestine	intestine
50	chr2:73612400-73614200	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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