Variant report

Variant	rs17217431
Chromosome Location	chr4:104113418-104113419
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:104112226..104114859-chr4:104116594..104119520,2	K562	blood:
2	chr4:104097079..104099003-chr4:104112349..104113938,2	MCF-7	breast:
3	chr4:104104486..104106664-chr4:104111970..104114594,2	K562	blood:

Variant related genes	Relation type
ENSG00000138778	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10516498	0.89[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs1054707	0.93[ASN][1000 genomes]
rs11724309	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11724466	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11724522	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11725048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11727029	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11729856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11730764	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11730765	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11734318	0.90[ASN][1000 genomes]
rs11737673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12500951	0.93[ASN][1000 genomes]
rs12504143	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12504262	0.89[CHB][hapmap];0.87[ASN][1000 genomes]
rs12505289	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12505908	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]
rs12506065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12506157	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12506198	0.94[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]
rs12507348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12508269	0.88[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs12511516	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12512468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1381657	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1381658	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17215694	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs17215785	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17215862	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17217592	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17283027	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17283077	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17283194	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17522932	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2306478	1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs2866633	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35714833	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3756268	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3756269	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs3765086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3775972	1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs3796982	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3796983	0.89[CHB][hapmap];0.86[ASN][1000 genomes]
rs3974474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55895342	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56126326	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56138287	0.81[ASN][1000 genomes]
rs56256243	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56378042	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56412006	0.87[ASN][1000 genomes]
rs58648171	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58888668	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59192877	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59341670	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61355145	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6533057	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66869812	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6822891	0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6825519	0.89[CHB][hapmap];0.87[ASN][1000 genomes]
rs6830791	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6836162	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6837114	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6840401	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72665040	0.93[ASN][1000 genomes]
rs72665042	0.93[ASN][1000 genomes]
rs72665048	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72665052	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72665054	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72665056	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72665063	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72665071	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72665093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72665096	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72666812	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs736048	0.93[ASN][1000 genomes]
rs746829	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7662455	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7664021	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7666067	1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs7668568	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7675057	0.86[ASN][1000 genomes]
rs7686105	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7690059	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	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
2	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
3	nsv830022	chr4:104087199-104257784	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs17217431	BDH2	cis	Nerve Tibial	GTEx
rs17217431	BDH2	Cis_1M	lymphoblastoid	RTeQTL
rs17217431	BDH2	cis	Artery Tibial	GTEx
rs17217431	BDH2	cis	lung	GTEx
rs17217431	BDH2	cis	Thyroid	GTEx
rs17217431	BDH2	cis	Esophagus Muscularis	GTEx
rs17217431	BDH2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:104058200-104118400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr4:104073600-104118400	Weak transcription	Fetal Kidney	kidney
3	chr4:104089800-104114800	Weak transcription	Placenta	Placenta
4	chr4:104089800-104118200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:104089800-104119000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:104090000-104118000	Weak transcription	Fetal Stomach	stomach
7	chr4:104090000-104118600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr4:104090000-104119000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr4:104090200-104118200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr4:104090200-104118200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:104090200-104118200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:104090200-104118200	Weak transcription	Fetal Intestine Small	intestine
13	chr4:104090400-104118200	Weak transcription	Fetal Brain Male	brain
14	chr4:104090600-104117600	Weak transcription	Fetal Heart	heart
15	chr4:104090800-104118200	Weak transcription	Duodenum Mucosa	Duodenum
16	chr4:104095200-104118800	Weak transcription	Adipose Nuclei	Adipose
17	chr4:104097000-104119000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr4:104099000-104118200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr4:104099200-104118200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr4:104099400-104118200	Weak transcription	Fetal Brain Female	brain
21	chr4:104099600-104118200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr4:104100400-104118200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:104100800-104118400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr4:104101000-104118400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr4:104101600-104118200	Weak transcription	Fetal Intestine Large	intestine
26	chr4:104102200-104118000	Weak transcription	HepG2	liver
27	chr4:104102200-104118200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr4:104104400-104115000	Weak transcription	Brain Substantia Nigra	brain
29	chr4:104104600-104119000	Weak transcription	Ovary	ovary
30	chr4:104105400-104117800	Weak transcription	Osteobl	bone
31	chr4:104106200-104116800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr4:104106800-104119000	Weak transcription	Stomach Mucosa	stomach
33	chr4:104107600-104115000	Weak transcription	Hela-S3	cervix
34	chr4:104108200-104116800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr4:104108200-104117800	Weak transcription	NHLF	lung
36	chr4:104108200-104118000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr4:104108200-104118000	Weak transcription	Thymus	Thymus
38	chr4:104108200-104118200	Weak transcription	Primary B cells from cord blood	blood
39	chr4:104112000-104117200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr4:104112600-104117800	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr4:104113000-104113800	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr4:104113000-104113800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr4:104113000-104113800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr4:104113000-104113800	Strong transcription	Fetal Lung	lung
45	chr4:104113000-104113800	Strong transcription	Fetal Muscle Trunk	muscle
46	chr4:104113000-104113800	Strong transcription	Fetal Muscle Leg	muscle
47	chr4:104113000-104113800	Strong transcription	NHDF-Ad	bronchial
48	chr4:104113000-104114000	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr4:104113000-104114000	Strong transcription	NH-A	brain
50	chr4:104113000-104115000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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