Variant report

Variant	rs6852715
Chromosome Location	chr4:99825639-99825640
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:99825075..99827998-chr4:99830736..99833783,3	K562	blood:
2	chr4:99825546..99827569-chr4:99849518..99851861,2	MCF-7	breast:
3	chr4:99818828..99820512-chr4:99824506..99827559,4	MCF-7	breast:
4	chr4:99821499..99832064-chr4:99845860..99851281,12	MCF-7	breast:
5	chr4:99825609..99828842-chr4:99829565..99832831,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000263923	Chromatin interaction
ENSG00000151247	Chromatin interaction
ENSG00000238449	Chromatin interaction
ENSG00000249055	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10004975	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10023577	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1037475	0.85[CEU][hapmap]
rs10433890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11097640	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11097643	0.85[CEU][hapmap]
rs11097645	0.84[CEU][hapmap]
rs11723037	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11725932	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs11729285	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11731878	0.85[CEU][hapmap]
rs12374261	0.85[CEU][hapmap]
rs12498533	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12644580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.80[YRI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1453871	0.85[CEU][hapmap]
rs17028293	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs17216446	0.85[CEU][hapmap]
rs1869459	0.85[CEU][hapmap]
rs2100426	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28494580	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28577966	0.84[EUR][1000 genomes]
rs2924581	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34830689	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35447189	0.85[EUR][1000 genomes]
rs4264834	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4699688	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4699693	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6810489	0.96[CEU][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs6811070	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6830125	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs6846221	0.81[CEU][hapmap];0.87[JPT][hapmap]
rs6846475	0.85[CEU][hapmap]
rs7660937	0.85[EUR][1000 genomes]
rs7661487	0.86[EUR][1000 genomes]
rs7664964	0.92[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs7665587	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7665590	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7674319	0.85[CEU][hapmap]
rs7674742	0.81[CEU][hapmap];0.87[JPT][hapmap]
rs7690818	0.85[CEU][hapmap]
rs7696573	0.85[CEU][hapmap]
rs7696584	0.85[CEU][hapmap]
rs9332467	0.88[CEU][hapmap];0.83[TSI][hapmap]
rs9996959	0.86[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	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv879654	chr4:99748988-99877402	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv879655	chr4:99783733-99843113	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6852715	ADH5	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99796000-99826400	Weak transcription	Right Ventricle	heart
2	chr4:99797000-99826600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr4:99801600-99829400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr4:99802800-99830200	Weak transcription	Ovary	ovary
5	chr4:99802800-99849000	Weak transcription	Aorta	Aorta
6	chr4:99804400-99848800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr4:99804600-99838400	Weak transcription	Esophagus	oesophagus
8	chr4:99805200-99832000	Weak transcription	Spleen	Spleen
9	chr4:99807200-99849000	Weak transcription	Colonic Mucosa	Colon
10	chr4:99807400-99826400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr4:99807800-99832000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:99808000-99841400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr4:99808600-99830600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr4:99808600-99849000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:99812200-99826400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr4:99813400-99825800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr4:99815800-99848200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr4:99816600-99826400	Weak transcription	NHDF-Ad	bronchial
19	chr4:99816600-99831200	Weak transcription	Brain Anterior Caudate	brain
20	chr4:99816600-99847200	Weak transcription	Fetal Brain Male	brain
21	chr4:99817000-99830800	Weak transcription	Brain Germinal Matrix	brain
22	chr4:99819000-99831000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr4:99819200-99829400	Weak transcription	Fetal Brain Female	brain
24	chr4:99819600-99826400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr4:99820600-99826800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr4:99822200-99829800	Weak transcription	A549	lung
27	chr4:99822400-99826600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr4:99822400-99826600	Weak transcription	HSMMtube	muscle
29	chr4:99822800-99829400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr4:99822800-99830000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr4:99822800-99830600	Weak transcription	Left Ventricle	heart
32	chr4:99822800-99831800	Weak transcription	Fetal Stomach	stomach
33	chr4:99823000-99826000	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr4:99823000-99826600	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr4:99823000-99826600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr4:99823000-99826600	Weak transcription	Fetal Intestine Large	intestine
37	chr4:99823000-99826600	Weak transcription	NHLF	lung
38	chr4:99823000-99826600	Weak transcription	Osteobl	bone
39	chr4:99823000-99826800	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr4:99823000-99826800	Weak transcription	HSMM	muscle
41	chr4:99823000-99826800	Weak transcription	NH-A	brain
42	chr4:99823000-99827400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr4:99823000-99828800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr4:99823000-99828800	Weak transcription	HUVEC	blood vessel
45	chr4:99823000-99829400	Weak transcription	Duodenum Mucosa	Duodenum
46	chr4:99823000-99829400	Weak transcription	Fetal Kidney	kidney
47	chr4:99823000-99829400	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr4:99823000-99830000	Weak transcription	Liver	Liver
49	chr4:99823000-99835600	Weak transcription	Adipose Nuclei	Adipose
50	chr4:99823000-99836000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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