Variant report

Variant	rs10004753
Chromosome Location	chr4:99447433-99447434
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:99446603..99448154-chr4:99449799..99451915,2	K562	blood:
2	chr4:99445632..99448103-chr4:99449993..99451915,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10002696	0.81[CHB][hapmap]
rs10005781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10006366	0.81[CHB][hapmap]
rs10025051	0.81[CHB][hapmap]
rs10516433	0.90[YRI][hapmap];0.81[AFR][1000 genomes]
rs10516434	0.94[YRI][hapmap];0.82[AFR][1000 genomes]
rs13108940	0.81[CHB][hapmap]
rs13116201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13435698	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1358548	0.83[JPT][hapmap]
rs17191936	0.92[CEU][hapmap]
rs17192060	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs17564872	0.90[YRI][hapmap]
rs17564998	0.82[AFR][1000 genomes]
rs1893714	0.84[JPT][hapmap]
rs2091547	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs34951629	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4699343	0.81[CHB][hapmap]
rs4699639	0.81[CHB][hapmap]
rs4699640	0.81[CHB][hapmap]
rs4699642	0.86[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6532740	0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs6830136	0.82[AFR][1000 genomes]
rs6840610	0.90[YRI][hapmap];0.80[AFR][1000 genomes]
rs6844261	0.89[JPT][hapmap]
rs6853079	0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs7667608	0.82[AFR][1000 genomes]
rs7668981	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs7688849	0.82[AFR][1000 genomes]
rs7689116	0.82[AFR][1000 genomes]
rs7689289	0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs7695093	0.93[CEU][hapmap];0.84[EUR][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	nsv529623	chr4:98501338-99460166	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv2754250	chr4:99094922-99527122	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1004181	chr4:99208152-99529576	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10004753	ADH7	cis	brain	seeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99438800-99452000	Enhancers	Fetal Heart	heart
2	chr4:99440400-99458400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:99442200-99450600	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr4:99444400-99448800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr4:99444600-99450200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr4:99444800-99448600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr4:99445200-99451800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr4:99445200-99461800	Weak transcription	HMEC	breast
9	chr4:99445400-99448800	Weak transcription	HSMM	muscle
10	chr4:99445400-99465400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr4:99445600-99447800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr4:99445600-99448000	Weak transcription	Brain Substantia Nigra	brain
13	chr4:99445600-99449800	Weak transcription	NHLF	lung
14	chr4:99445600-99450000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr4:99445600-99450200	Weak transcription	Gastric	stomach
16	chr4:99445800-99447800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr4:99445800-99448800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr4:99445800-99450000	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr4:99446000-99448200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr4:99446000-99449000	Weak transcription	NHEK	skin
21	chr4:99446000-99449800	Weak transcription	Colon Smooth Muscle	Colon
22	chr4:99446000-99467400	Weak transcription	Fetal Stomach	stomach
23	chr4:99446200-99448800	Enhancers	Ovary	ovary
24	chr4:99446600-99448600	Weak transcription	Osteobl	bone
25	chr4:99446600-99448800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:99446600-99448800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr4:99446600-99450200	Weak transcription	NH-A	brain
28	chr4:99446800-99447800	Weak transcription	NHDF-Ad	bronchial
29	chr4:99446800-99448800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:99446800-99449800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr4:99446800-99451200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr4:99446800-99457400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr4:99446800-99461600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr4:99447200-99447600	Enhancers	Brain Germinal Matrix	brain
35	chr4:99447200-99447600	Enhancers	Fetal Intestine Small	intestine
36	chr4:99447200-99447800	Enhancers	Brain Angular Gyrus	brain
37	chr4:99447400-99447600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr4:99447400-99448200	Enhancers	Fetal Brain Male	brain
39	chr4:99447400-99448800	Weak transcription	Brain Anterior Caudate	brain
40	chr4:99447400-99449400	Enhancers	Fetal Brain Female	brain
41	chr4:99447400-99450200	Enhancers	Brain Hippocampus Middle	brain

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