Variant report

Variant	rs12223
Chromosome Location	chr6:114183884-114183885
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:114183529..114185723-chr6:114208542..114210250,2	MCF-7	breast:
2	chr6:114180592..114182407-chr6:114183261..114185207,2	MCF-7	breast:
3	chr6:113964552..113967035-chr6:114182588..114184413,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10499076	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11153451	0.81[YRI][hapmap]
rs11153452	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1322455	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2169507	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs352079	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4562174	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4945504	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4945977	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4945979	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4945981	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6919507	0.87[JPT][hapmap]
rs7751759	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7763868	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9320472	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9374431	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1021774	chr6:114063971-114407280	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv538422	chr6:114063971-114407280	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv3363275	chr6:114101331-114302866	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv482098	chr6:114178527-114184652	Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12223	FRK	cis	parietal	SCAN
rs12223	ZUFSP	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:114175600-114184000	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr6:114179400-114184200	Active TSS	Fetal Brain Female	brain
3	chr6:114181000-114184000	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:114181000-114184600	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:114181000-114200200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:114181200-114184000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
7	chr6:114181200-114193200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr6:114181600-114184000	Transcr. at gene 5' and 3'	NH-A	brain
9	chr6:114181600-114184200	Strong transcription	Primary B cells from peripheral blood	blood
10	chr6:114181800-114184000	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr6:114181800-114184200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:114181800-114184200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:114181800-114186000	Weak transcription	Lung	lung
14	chr6:114181800-114193200	Weak transcription	Liver	Liver
15	chr6:114181800-114194200	Weak transcription	Pancreas	Pancrea
16	chr6:114182000-114184400	Strong transcription	Fetal Thymus	thymus
17	chr6:114182000-114187400	Weak transcription	Colonic Mucosa	Colon
18	chr6:114182200-114184200	Genic enhancers	HSMM	muscle
19	chr6:114182200-114184400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr6:114182200-114192600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr6:114182200-114194200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr6:114182200-114194200	Weak transcription	Ovary	ovary
23	chr6:114182400-114184000	Strong transcription	Placenta	Placenta
24	chr6:114182400-114184200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:114182400-114193000	Weak transcription	Fetal Intestine Small	intestine
26	chr6:114182400-114193200	Weak transcription	Fetal Intestine Large	intestine
27	chr6:114182600-114184400	Genic enhancers	Fetal Lung	lung
28	chr6:114182600-114184600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr6:114182600-114185200	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr6:114182600-114193000	Weak transcription	HepG2	liver
31	chr6:114182800-114184000	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr6:114182800-114184000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr6:114182800-114184000	Genic enhancers	Fetal Kidney	kidney
34	chr6:114182800-114184200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:114182800-114193000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr6:114183000-114184200	Genic enhancers	Muscle Satellite Cultured Cells	--
37	chr6:114183000-114184200	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
38	chr6:114183000-114184400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr6:114183000-114184400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:114183000-114185800	Weak transcription	Fetal Stomach	stomach
41	chr6:114183200-114185400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr6:114183200-114196200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr6:114183400-114184000	Genic enhancers	Duodenum Smooth Muscle	Duodenum
44	chr6:114183400-114184000	Genic enhancers	Rectal Mucosa Donor 31	rectum
45	chr6:114183400-114184200	Strong transcription	Primary B cells from cord blood	blood
46	chr6:114183400-114184200	Weak transcription	Brain Angular Gyrus	brain
47	chr6:114183400-114184200	Genic enhancers	Fetal Brain Male	brain
48	chr6:114183600-114184000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr6:114183600-114184000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr6:114183600-114184000	Enhancers	Brain Hippocampus Middle	brain

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