Variant report

Variant	rs2064591
Chromosome Location	chr6:56421463-56421464
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56416932..56418493-chr6:56421401..56422998,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs11753813	0.91[CEU][hapmap]
rs11756977	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11759493	0.81[CEU][hapmap]
rs13194746	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13219448	0.88[EUR][1000 genomes]
rs1535612	0.91[CEU][hapmap]
rs16887974	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2273973	0.91[CEU][hapmap]
rs4130060	0.81[CEU][hapmap]
rs4143827	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4143828	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs4236139	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4236140	0.81[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs4236141	0.91[CEU][hapmap];0.93[EUR][1000 genomes]
rs4236142	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4236143	0.81[EUR][1000 genomes]
rs4236144	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs4236145	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs4283892	0.81[CEU][hapmap]
rs4329120	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4346846	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4454141	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4466244	0.93[EUR][1000 genomes]
rs4472350	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4473850	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4499917	0.81[CEU][hapmap]
rs4712132	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs4712133	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4715626	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4715627	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4715628	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4715629	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4715630	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs4715631	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6459161	0.81[CEU][hapmap]
rs6904202	0.90[CEU][hapmap];0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs6906792	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6907917	0.83[EUR][1000 genomes]
rs6914184	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6919608	0.95[CEU][hapmap];0.90[CHB][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6922770	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6939305	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7741295	0.81[CEU][hapmap]
rs7743011	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7755361	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7755573	0.81[EUR][1000 genomes]
rs7759875	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7760640	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7760695	0.82[EUR][1000 genomes]
rs7761281	0.90[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7762629	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs9296848	0.81[CEU][hapmap]
rs9296849	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9296850	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs9349826	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9357921	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs9357922	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs9370533	0.80[CEU][hapmap]
rs9396220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475713	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9475714	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv885912	chr6:56327849-56458836	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2064591	COL21A1	cis	cerebellar cortex	BrainEAC

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56408200-56440400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:56408200-56440600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:56408200-56496000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:56408400-56430800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr6:56413800-56458400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr6:56415400-56427000	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr6:56415800-56426000	Weak transcription	Ovary	ovary
8	chr6:56415800-56435200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:56416200-56423000	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr6:56416400-56424200	Strong transcription	GM12878-XiMat	blood
11	chr6:56416400-56426800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:56416400-56427000	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr6:56417000-56427800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr6:56417000-56516400	Weak transcription	Pancreas	Pancrea
15	chr6:56417200-56462000	Weak transcription	Lung	lung
16	chr6:56417200-56481400	Weak transcription	Esophagus	oesophagus
17	chr6:56417400-56422200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:56417400-56426400	Strong transcription	HMEC	breast
19	chr6:56417400-56430000	Weak transcription	Fetal Intestine Small	intestine
20	chr6:56417400-56435400	Weak transcription	HepG2	liver
21	chr6:56417600-56426800	Strong transcription	Liver	Liver
22	chr6:56417800-56426800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr6:56417800-56430400	Weak transcription	Fetal Muscle Trunk	muscle
24	chr6:56417800-56454200	Weak transcription	Psoas Muscle	Psoas
25	chr6:56417800-56455400	Weak transcription	Gastric	stomach
26	chr6:56418000-56430200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr6:56418000-56435400	Weak transcription	Fetal Brain Male	brain
28	chr6:56418200-56426400	Strong transcription	NHDF-Ad	bronchial
29	chr6:56418200-56430800	Weak transcription	NHLF	lung
30	chr6:56418400-56423600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr6:56418400-56426400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr6:56418400-56426400	Strong transcription	NH-A	brain
33	chr6:56418400-56427000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:56418800-56427200	Strong transcription	Osteobl	bone
35	chr6:56419600-56422200	Genic enhancers	HSMM	muscle
36	chr6:56419600-56422400	Genic enhancers	Fetal Lung	lung
37	chr6:56419800-56426400	Strong transcription	HUVEC	blood vessel
38	chr6:56420000-56421800	Enhancers	Rectal Smooth Muscle	rectum
39	chr6:56420000-56425600	Weak transcription	Placenta	Placenta
40	chr6:56420400-56423400	Weak transcription	Brain Anterior Caudate	brain
41	chr6:56420400-56426000	Weak transcription	Brain Cingulate Gyrus	brain
42	chr6:56420400-56429400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:56420400-56430200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr6:56420400-56430800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:56420400-56434800	Weak transcription	Brain Germinal Matrix	brain
46	chr6:56420400-56457400	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr6:56420600-56421600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr6:56420600-56422000	Weak transcription	Brain Angular Gyrus	brain
49	chr6:56420600-56422000	Enhancers	Colon Smooth Muscle	Colon
50	chr6:56420600-56422000	Weak transcription	Fetal Muscle Leg	muscle

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