Variant report

Variant	rs12576603
Chromosome Location	chr11:36178090-36178091
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:36177041..36178787-chr11:36285024..36287447,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1001715	1.00[LWK][hapmap]
rs10836507	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11033442	1.00[LWK][hapmap];1.00[MKK][hapmap]
rs11033457	0.89[GIH][hapmap];0.84[MKK][hapmap];0.85[TSI][hapmap]
rs11033501	1.00[LWK][hapmap]
rs11551023	1.00[LWK][hapmap]
rs11602141	1.00[LWK][hapmap]
rs11603810	1.00[LWK][hapmap]
rs12222421	0.89[GIH][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap]
rs12421199	1.00[LWK][hapmap]
rs16928451	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16928462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55918021	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56370337	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7111826	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs72935533	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs872534	1.00[LWK][hapmap]

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	nsv467791	chr11:36108497-36999385	Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv554003	chr11:36108497-36999385	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv897225	chr11:36136912-36244190	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12576603	LDLRAD3	cis	parietal	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:36169000-36178200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr11:36171400-36184000	Weak transcription	Right Atrium	heart
3	chr11:36171600-36187800	Weak transcription	Spleen	Spleen
4	chr11:36172000-36184000	Weak transcription	Pancreas	Pancrea
5	chr11:36172000-36184200	Weak transcription	Fetal Intestine Small	intestine
6	chr11:36172600-36183400	Weak transcription	Hela-S3	cervix
7	chr11:36172600-36190400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr11:36173000-36183200	Weak transcription	HSMMtube	muscle
9	chr11:36173600-36179600	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr11:36174600-36178400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr11:36174600-36179600	Enhancers	Ovary	ovary
12	chr11:36175000-36180000	Enhancers	Fetal Lung	lung
13	chr11:36175000-36184000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr11:36175200-36179600	Enhancers	Fetal Stomach	stomach
15	chr11:36175200-36183800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr11:36175400-36178400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr11:36175400-36181400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr11:36175600-36184000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr11:36175600-36184200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr11:36175800-36179200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr11:36175800-36179800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr11:36175800-36180000	Enhancers	Fetal Muscle Leg	muscle
23	chr11:36176000-36179800	Enhancers	HUVEC	blood vessel
24	chr11:36176200-36178400	Enhancers	Fetal Kidney	kidney
25	chr11:36176200-36179400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr11:36176400-36178600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr11:36176400-36179000	Enhancers	Fetal Brain Female	brain
28	chr11:36176400-36179200	Enhancers	NHLF	lung
29	chr11:36176400-36179400	Enhancers	NHDF-Ad	bronchial
30	chr11:36176600-36178600	Weak transcription	Left Ventricle	heart
31	chr11:36176600-36179200	Enhancers	Brain Cingulate Gyrus	brain
32	chr11:36176600-36184000	Weak transcription	Right Ventricle	heart
33	chr11:36176800-36178600	Enhancers	Pancreatic Islets	Pancreatic Islet
34	chr11:36176800-36181400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr11:36176800-36181400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr11:36177200-36178200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr11:36177200-36178200	Weak transcription	Fetal Heart	heart
38	chr11:36177200-36178800	Enhancers	Stomach Smooth Muscle	stomach
39	chr11:36177200-36179400	Enhancers	Muscle Satellite Cultured Cells	--
40	chr11:36177200-36179400	Enhancers	HSMM	muscle
41	chr11:36177200-36179600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr11:36177400-36178400	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr11:36177400-36179000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr11:36177400-36179000	Enhancers	HMEC	breast
45	chr11:36177400-36179600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr11:36177600-36178200	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr11:36177600-36178200	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr11:36177600-36178400	Flanking Active TSS	Brain Hippocampus Middle	brain
49	chr11:36177600-36178400	Flanking Active TSS	Brain Substantia Nigra	brain
50	chr11:36177600-36178400	Flanking Active TSS	Fetal Brain Male	brain

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