Variant report

Variant	rs6811482
Chromosome Location	chr4:57358701-57358702
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57357731..57359381-chr4:57360011..57362560,2	MCF-7	breast:
2	chr4:57351584..57356949-chr4:57358180..57362673,6	MCF-7	breast:
3	chr4:57347619..57349787-chr4:57358625..57362787,3	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10007967	0.93[EUR][1000 genomes]
rs10015634	0.91[CEU][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs10518	0.91[CEU][hapmap];0.81[LWK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10866433	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs11133439	0.91[JPT][hapmap]
rs11610	0.94[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11724302	0.95[JPT][hapmap]
rs12646703	0.94[ASW][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12648503	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13141793	0.91[JPT][hapmap]
rs1356787	0.94[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.80[TSI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17086793	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17086803	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs17086832	0.88[YRI][hapmap]
rs17086883	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17086887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292985	0.95[JPT][hapmap]
rs28472763	0.84[EUR][1000 genomes]
rs4073691	0.86[EUR][1000 genomes]
rs4383672	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4524447	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4615235	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4616819	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4865090	0.95[JPT][hapmap]
rs4865104	0.88[EUR][1000 genomes]
rs4865105	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4865110	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57523479	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6554348	0.95[JPT][hapmap]
rs6554349	0.95[JPT][hapmap]
rs6584	0.94[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs66599079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68101565	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6811821	0.90[CEU][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs6816218	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6816268	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6818715	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6820417	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6830518	0.94[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.80[TSI][hapmap];0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6832168	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6842307	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6843587	0.86[EUR][1000 genomes]
rs6848187	1.00[ASW][hapmap];0.91[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7670198	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7689163	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs7692385	0.95[JPT][hapmap]
rs7693137	0.95[JPT][hapmap]
rs7700034	0.81[CEU][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs9312675	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6811482	SRP72	cis	normal skin	skin_eQTL
rs6811482	SRP72	Cis_1M	lymphoblastoid	RTeQTL
rs6811482	SRP72	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57334800-57364000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:57334800-57371200	Weak transcription	Stomach Mucosa	stomach
3	chr4:57335200-57371400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr4:57335600-57370200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr4:57335800-57359000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr4:57335800-57365600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:57335800-57369200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr4:57335800-57370200	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr4:57335800-57370800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr4:57336000-57362200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr4:57336000-57362600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:57336000-57364200	Strong transcription	Osteobl	bone
13	chr4:57336000-57369400	Strong transcription	Liver	Liver
14	chr4:57336000-57369800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:57336000-57370000	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr4:57336000-57370000	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr4:57336000-57370200	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr4:57336000-57371000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:57336200-57365000	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr4:57336200-57369200	Strong transcription	Fetal Thymus	thymus
21	chr4:57336200-57370000	Strong transcription	Placenta	Placenta
22	chr4:57336200-57370400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr4:57336400-57364800	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr4:57336400-57365400	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr4:57336400-57368200	Strong transcription	Fetal Muscle Trunk	muscle
26	chr4:57336400-57369200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr4:57336400-57369200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr4:57336400-57370200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr4:57336600-57360400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr4:57336600-57364200	Strong transcription	Dnd41	blood
31	chr4:57336600-57365400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr4:57336600-57369200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr4:57337200-57363800	Strong transcription	Duodenum Mucosa	Duodenum
34	chr4:57337200-57365400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr4:57337200-57369200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr4:57337400-57359000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr4:57337600-57364000	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr4:57337600-57364800	Strong transcription	Fetal Intestine Large	intestine
39	chr4:57337800-57362400	Strong transcription	Primary B cells from cord blood	blood
40	chr4:57337800-57363200	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr4:57337800-57365600	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr4:57337800-57369200	Strong transcription	Adipose Nuclei	Adipose
43	chr4:57337800-57369400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr4:57338000-57365000	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr4:57338200-57364200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr4:57340600-57366600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr4:57340800-57369000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr4:57342000-57370200	Strong transcription	Primary B cells from peripheral blood	blood
49	chr4:57342400-57370800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr4:57342400-57371400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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