Variant report

Variant	rs17046546
Chromosome Location	chr3:67583238-67583239
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:67566852..67569780-chr3:67581868..67584034,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11919650	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11919747	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11923127	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11926543	0.86[YRI][hapmap]
rs11927204	0.93[EUR][1000 genomes]
rs12488930	0.98[EUR][1000 genomes]
rs12489287	0.89[EUR][1000 genomes]
rs12495506	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12636825	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13087877	0.82[AFR][1000 genomes]
rs17046528	0.98[EUR][1000 genomes]
rs17046548	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4371532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4856869	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4856870	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4856872	0.95[EUR][1000 genomes]
rs4856873	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs4856874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4856875	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5028414	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56020437	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56246741	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56361934	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58093651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61386974	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6548615	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6768958	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6784255	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72923195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72924913	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7623441	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007093	chr3:67113534-67602973	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv470638	chr3:67367341-67814738	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv460700	chr3:67393629-67712970	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription 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 target site	10 gene(s)	inside rSNPs	diseases
4	nsv590560	chr3:67393629-67712970	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv834719	chr3:67396626-67589852	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv1012416	chr3:67546244-67615531	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv590561	chr3:67548852-67690626	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:67560600-67586200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:67560600-67620800	Weak transcription	Esophagus	oesophagus
3	chr3:67565600-67595800	Weak transcription	Fetal Kidney	kidney
4	chr3:67568000-67590600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:67576200-67585400	Enhancers	NHDF-Ad	bronchial
6	chr3:67578200-67585600	Weak transcription	Psoas Muscle	Psoas
7	chr3:67578200-67600400	Weak transcription	Lung	lung
8	chr3:67578200-67612400	Weak transcription	Spleen	Spleen
9	chr3:67578200-67634600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:67578400-67583800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:67578400-67593800	Weak transcription	Fetal Intestine Small	intestine
12	chr3:67578600-67601800	Weak transcription	Left Ventricle	heart
13	chr3:67579200-67586200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr3:67579200-67603400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:67579200-67608800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr3:67579200-67620600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr3:67579400-67585000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr3:67579400-67585800	Weak transcription	Right Ventricle	heart
19	chr3:67579400-67586000	Enhancers	Muscle Satellite Cultured Cells	--
20	chr3:67579400-67586200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr3:67579400-67588400	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr3:67579400-67590800	Weak transcription	Fetal Stomach	stomach
23	chr3:67579400-67591000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:67579400-67598200	Weak transcription	Aorta	Aorta
25	chr3:67579400-67600600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr3:67579400-67623000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr3:67579400-67633800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr3:67579400-67657600	Weak transcription	Pancreas	Pancrea
29	chr3:67579600-67588600	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr3:67579600-67601000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr3:67579600-67601800	Weak transcription	Fetal Intestine Large	intestine
32	chr3:67579600-67601800	Weak transcription	Ovary	ovary
33	chr3:67579800-67586200	Weak transcription	Primary B cells from peripheral blood	blood
34	chr3:67579800-67588600	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr3:67580000-67606400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr3:67580600-67591200	Weak transcription	Primary T cells from cord blood	blood
37	chr3:67580800-67620200	Weak transcription	GM12878-XiMat	blood
38	chr3:67581000-67584200	Enhancers	Pancreatic Islets	Pancreatic Islet
39	chr3:67581600-67587600	Weak transcription	Primary B cells from cord blood	blood
40	chr3:67582000-67585800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:67582000-67590800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:67582000-67601600	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr3:67582200-67583400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:67582200-67583400	Weak transcription	Osteobl	bone
45	chr3:67582200-67583800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:67582200-67583800	Weak transcription	HSMM	muscle
47	chr3:67582200-67637000	Weak transcription	Rectal Smooth Muscle	rectum
48	chr3:67582400-67583400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr3:67582400-67585800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr3:67582400-67596400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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