Variant report

Variant	rs12505908
Chromosome Location	chr4:104048353-104048354
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	chr4:104048242..104049132-chr5:141740006..141740887,2	HCT-116	colon:

Extended variants
information (count: 90 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10516498	0.89[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];0.85[TSI][hapmap];1.00[ASN][1000 genomes]
rs1054707	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11724309	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11724466	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11724522	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11725048	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11727029	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11729856	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11730764	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11730765	0.87[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734318	0.97[ASN][1000 genomes]
rs11737673	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12500951	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12504143	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12504262	0.89[CHB][hapmap];0.94[ASN][1000 genomes]
rs12505289	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506065	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506157	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506198	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12507348	0.81[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]
rs12508269	0.88[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs12511516	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12512468	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1381657	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1381658	0.81[CEU][hapmap];0.87[CHB][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17215694	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17215785	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17215862	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17217431	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17217592	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17283027	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17283077	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17283194	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17522932	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2045746	0.81[YRI][hapmap]
rs2306478	1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs2720469	0.94[CHD][hapmap];0.88[GIH][hapmap]
rs2866633	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35714833	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756268	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3756269	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3765086	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3775972	1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs3796982	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796983	0.89[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.93[ASN][1000 genomes]
rs3974474	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4699050	0.81[YRI][hapmap]
rs55895342	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56126326	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56256243	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56378042	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56412006	0.94[ASN][1000 genomes]
rs58648171	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58888668	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59192877	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59341670	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61355145	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6533057	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66869812	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6822891	0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6825519	0.89[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.94[ASN][1000 genomes]
rs6830791	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6836162	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6837114	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6840401	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665040	1.00[ASN][1000 genomes]
rs72665042	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665048	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665052	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665054	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665056	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665063	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72665071	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72665093	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72665096	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72666812	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs736048	1.00[ASN][1000 genomes]
rs746829	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7662455	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7664021	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7666067	1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs7668568	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7675057	0.94[CHD][hapmap];0.81[GIH][hapmap];0.93[ASN][1000 genomes]
rs7686105	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7690059	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757946	chr4:103780705-104057321	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers 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	36 gene(s)	inside rSNPs	diseases
2	esv2759270	chr4:103780705-104057321	ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv3429917	chr4:103915319-104207455	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS 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 miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv830021	chr4:103934454-104100588	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv1015023	chr4:104039145-104565217	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12505908	BDH2	cis	cerebellum	SCAN
rs12505908	BDH2	cis	Esophagus Mucosa	GTEx
rs12505908	BDH2	cis	Skin Sun Exposed Lower leg	GTEx
rs12505908	BDH2	Cis_1M	lymphoblastoid	RTeQTL
rs12505908	BDH2	cis	lung	GTEx
rs12505908	PPP3CA	cis	parietal	SCAN
rs12505908	BDH2	cis	Artery Tibial	GTEx
rs12505908	BDH2	cis	Nerve Tibial	GTEx
rs12505908	BDH2	cis	Esophagus Muscularis	GTEx
rs12505908	BDH2	cis	Thyroid	GTEx

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:104021000-104049200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr4:104021000-104049200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr4:104021000-104056000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr4:104021000-104058200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr4:104021000-104063800	Weak transcription	Fetal Stomach	stomach
6	chr4:104021000-104068400	Weak transcription	Fetal Brain Male	brain
7	chr4:104021000-104076400	Weak transcription	Fetal Brain Female	brain
8	chr4:104021000-104089600	Weak transcription	Fetal Heart	heart
9	chr4:104021200-104076600	Weak transcription	Fetal Intestine Small	intestine
10	chr4:104021200-104100200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr4:104021400-104074600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr4:104029000-104056200	Weak transcription	Fetal Lung	lung
13	chr4:104029000-104089000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr4:104029800-104089000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:104030200-104063600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr4:104030200-104089600	Weak transcription	Hela-S3	cervix
17	chr4:104030400-104049400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr4:104030400-104053000	Weak transcription	Fetal Muscle Trunk	muscle
19	chr4:104030800-104055800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr4:104031200-104069000	Weak transcription	Primary B cells from cord blood	blood
21	chr4:104031400-104053000	Weak transcription	Fetal Intestine Large	intestine
22	chr4:104031400-104057600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr4:104032000-104049200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr4:104032200-104053000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr4:104032200-104053000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr4:104032400-104049200	Weak transcription	A549	lung
27	chr4:104032400-104049200	Weak transcription	GM12878-XiMat	blood
28	chr4:104032600-104049400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:104032600-104050200	Weak transcription	Fetal Muscle Leg	muscle
30	chr4:104033200-104054200	Weak transcription	NH-A	brain
31	chr4:104034800-104049400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr4:104034800-104050800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:104035200-104057800	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr4:104036200-104050000	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr4:104038200-104095800	Strong transcription	Fetal Thymus	thymus
36	chr4:104039200-104058400	Weak transcription	Left Ventricle	heart
37	chr4:104039200-104077400	Strong transcription	Dnd41	blood
38	chr4:104040200-104049200	Weak transcription	NHDF-Ad	bronchial
39	chr4:104040200-104049600	Weak transcription	NHLF	lung
40	chr4:104041600-104053000	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr4:104043200-104049400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr4:104044600-104070600	Weak transcription	HepG2	liver
43	chr4:104044800-104053200	Weak transcription	K562	blood
44	chr4:104045000-104048800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:104045000-104049000	Weak transcription	Primary hematopoietic stem cells	blood
46	chr4:104045000-104049400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr4:104045000-104050200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr4:104045000-104050600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr4:104045000-104052000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr4:104045200-104049600	Weak transcription	Osteobl	bone

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