Variant report

Variant	rs4931215
Chromosome Location	chr12:29919461-29919462
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:29918838..29921011-chr12:29921108..29922618,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10743672	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10743673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10743674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10771578	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10771579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771580	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10843501	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10843502	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10843503	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10843504	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11609828	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12231167	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12810794	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1551930	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2882467	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs302335	0.93[ASW][hapmap];0.89[GIH][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs302336	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs302337	0.93[ASW][hapmap];0.89[GIH][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs302338	0.95[MEX][hapmap];0.92[AMR][1000 genomes]
rs4244848	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4244849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4931216	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4931217	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4931218	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4931219	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4931220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56703053	0.81[AMR][1000 genomes]
rs67168837	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7967779	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529328	chr12:29692414-30246209	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv898953	chr12:29905322-29989292	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4931215	FGFR1OP2	cis	parietal	SCAN
rs4931215	FAR2	cis	lymphoblastoid	seeQTL
rs4931215	TMTC1	cis	Whole Blood	GTEx
rs4931215	FGD4	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29880000-29921200	Weak transcription	Fetal Kidney	kidney
2	chr12:29898600-29921200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:29904200-29928600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr12:29904600-29927800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:29904800-29924200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr12:29906600-29928400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr12:29908800-29920800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:29908800-29925000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr12:29910400-29921400	Weak transcription	NHLF	lung
10	chr12:29910600-29921400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr12:29910600-29921400	Weak transcription	Osteobl	bone
12	chr12:29911800-29922200	Weak transcription	Ovary	ovary
13	chr12:29912000-29921400	Weak transcription	Fetal Stomach	stomach
14	chr12:29912800-29924000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:29915600-29919800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:29916000-29921800	Weak transcription	HSMMtube	muscle
17	chr12:29916000-29922400	Weak transcription	Esophagus	oesophagus
18	chr12:29916000-29931400	Weak transcription	Pancreas	Pancrea
19	chr12:29916200-29922400	Weak transcription	Lung	lung
20	chr12:29916400-29919600	Strong transcription	HSMM	muscle
21	chr12:29916400-29920200	Weak transcription	Brain Germinal Matrix	brain
22	chr12:29916400-29920800	Weak transcription	Brain Angular Gyrus	brain
23	chr12:29916400-29920800	Weak transcription	Fetal Lung	lung
24	chr12:29916400-29921800	Weak transcription	Brain Anterior Caudate	brain
25	chr12:29916600-29921200	Weak transcription	NHDF-Ad	bronchial
26	chr12:29916600-29921400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:29916600-29921400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr12:29916600-29923000	Weak transcription	Liver	Liver
29	chr12:29916800-29921400	Weak transcription	Right Atrium	heart
30	chr12:29916800-29921600	Weak transcription	Fetal Heart	heart
31	chr12:29916800-29922000	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr12:29916800-29922200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr12:29916800-29924400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr12:29916800-29925400	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr12:29917000-29921200	Weak transcription	Stomach Smooth Muscle	stomach
36	chr12:29917000-29921400	Weak transcription	Psoas Muscle	Psoas
37	chr12:29917000-29922000	Weak transcription	Brain Hippocampus Middle	brain
38	chr12:29917000-29922200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:29917000-29922200	Weak transcription	Spleen	Spleen
40	chr12:29917000-29924600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr12:29917000-29926000	Weak transcription	Right Ventricle	heart
42	chr12:29917600-29921400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr12:29918000-29921400	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr12:29918000-29924800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:29918600-29922200	Weak transcription	Small Intestine	intestine
46	chr12:29918800-29919600	Strong transcription	Colon Smooth Muscle	Colon
47	chr12:29918800-29919600	Strong transcription	Hela-S3	cervix
48	chr12:29918800-29919800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr12:29918800-29919800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr12:29918800-29919800	Strong transcription	Muscle Satellite Cultured Cells	--

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