Variant report

Variant	rs2169508
Chromosome Location	chr4:104066890-104066891
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BDH2-4	chr4:104066680-104066938	NONHSAT097626

Extended variants
information (count: 37 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1031804	0.94[CHB][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11727498	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12501621	0.94[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17217473	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2045746	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2069274	0.89[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2126470	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2251322	0.94[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2251634	0.94[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2615539	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2623060	0.93[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2623064	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2623070	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2711897	0.89[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2711898	0.94[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2711899	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2720448	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2720458	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2720460	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2720461	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2720462	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2720464	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2720468	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2720469	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2720471	0.89[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2866635	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4699050	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4699051	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6533056	0.89[CHB][hapmap];0.84[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6810571	0.94[CHB][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6813563	0.94[CHB][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6815783	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6841136	0.94[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6850461	0.94[CHB][hapmap];0.84[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[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	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
3	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2169508	BDH2	Cis_1M	lymphoblastoid	RTeQTL
rs2169508	BDH2	cis	Thyroid	GTEx
rs2169508	BDH2	cis	Esophagus Muscularis	GTEx
rs2169508	KRT8P46	cis	lung	GTEx
rs2169508	MANBA	Cis_1M	lymphoblastoid	RTeQTL
rs2169508	BDH2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:104021000-104068400	Weak transcription	Fetal Brain Male	brain
2	chr4:104021000-104076400	Weak transcription	Fetal Brain Female	brain
3	chr4:104021000-104089600	Weak transcription	Fetal Heart	heart
4	chr4:104021200-104076600	Weak transcription	Fetal Intestine Small	intestine
5	chr4:104021200-104100200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr4:104021400-104074600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr4:104029000-104089000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:104029800-104089000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:104030200-104089600	Weak transcription	Hela-S3	cervix
10	chr4:104031200-104069000	Weak transcription	Primary B cells from cord blood	blood
11	chr4:104038200-104095800	Strong transcription	Fetal Thymus	thymus
12	chr4:104039200-104077400	Strong transcription	Dnd41	blood
13	chr4:104044600-104070600	Weak transcription	HepG2	liver
14	chr4:104048600-104071400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr4:104049000-104073800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr4:104049000-104075200	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr4:104049600-104078200	Weak transcription	Brain Germinal Matrix	brain
18	chr4:104049800-104074400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr4:104050600-104085400	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr4:104050800-104071600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr4:104051000-104089200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr4:104051000-104092600	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr4:104051400-104089400	Weak transcription	Placenta	Placenta
24	chr4:104051600-104088800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr4:104051800-104076800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:104052000-104089200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr4:104052600-104088800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr4:104053200-104077400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr4:104054800-104069800	Weak transcription	Fetal Intestine Large	intestine
30	chr4:104055000-104073400	Weak transcription	Fetal Kidney	kidney
31	chr4:104055200-104067200	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr4:104055600-104089200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr4:104056800-104080000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr4:104057000-104068800	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr4:104057000-104069600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr4:104057600-104071200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr4:104058200-104067000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr4:104058200-104118400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr4:104058800-104079400	Weak transcription	Primary T cells from cord blood	blood
40	chr4:104059200-104071800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr4:104059400-104067400	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr4:104059400-104067400	Weak transcription	Fetal Muscle Leg	muscle
43	chr4:104059400-104087400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr4:104059400-104089000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr4:104059600-104067000	Weak transcription	Fetal Muscle Trunk	muscle
46	chr4:104060800-104074800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr4:104061000-104071000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr4:104061000-104071200	Strong transcription	HMEC	breast
49	chr4:104061000-104071400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr4:104061000-104072400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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