Variant report

Variant	rs704034
Chromosome Location	chr5:40842116-40842117
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:116184240..116184758-chr5:40841642..40842505,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000173218	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10064650	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1070444	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1070445	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10941528	1.00[YRI][hapmap]
rs1097592	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11740266	0.81[CEU][hapmap]
rs11745121	1.00[CEU][hapmap];0.88[GIH][hapmap];0.89[TSI][hapmap]
rs11746535	0.92[EUR][1000 genomes]
rs11748087	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11749180	0.88[GIH][hapmap];0.89[TSI][hapmap]
rs11749437	1.00[CEU][hapmap]
rs12186450	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs12188129	1.00[CEU][hapmap];0.88[GIH][hapmap];0.89[TSI][hapmap]
rs1501815	1.00[YRI][hapmap]
rs152374	1.00[JPT][hapmap]
rs1530811	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs154274	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs154276	1.00[JPT][hapmap]
rs154278	1.00[JPT][hapmap]
rs154282	1.00[JPT][hapmap]
rs154283	1.00[JPT][hapmap]
rs166282	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs187274	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs192962	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs249411	1.00[CHD][hapmap]
rs29737	1.00[JPT][hapmap]
rs29762	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs29763	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs29764	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs323556	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs323562	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3805217	1.00[YRI][hapmap]
rs42515	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs445367	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs455519	1.00[JPT][hapmap]
rs459491	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs459794	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs463675	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs463905	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs464045	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs62357568	0.89[EUR][1000 genomes]
rs62357569	0.93[EUR][1000 genomes]
rs62357570	0.94[EUR][1000 genomes]
rs62357571	0.94[EUR][1000 genomes]
rs62357574	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62357600	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs694217	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7702698	1.00[YRI][hapmap]
rs7715491	1.00[YRI][hapmap]
rs837102	1.00[JPT][hapmap]
rs837378	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs837385	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880438	chr5:40753877-40900717	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases
2	nsv597877	chr5:40796746-40848803	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	158 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs704034	CARD6	cis	Artery Tibial	GTEx
rs704034	GDNF	cis	cerebellum	SCAN
rs704034	ZNF131	cis	cerebellum	SCAN
rs704034	C5orf51	cis	cerebellum	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40836000-40843600	Weak transcription	Spleen	Spleen
2	chr5:40836000-40852600	Weak transcription	Small Intestine	intestine
3	chr5:40840800-40842800	Active TSS	Adipose Nuclei	Adipose
4	chr5:40841000-40842200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr5:40841000-40842200	Active TSS	Primary T cells fromperipheralblood	blood
6	chr5:40841000-40842400	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr5:40841000-40842800	Active TSS	Aorta	Aorta
8	chr5:40841000-40842800	Active TSS	Colon Smooth Muscle	Colon
9	chr5:40841000-40842800	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr5:40841000-40842800	Active TSS	Right Ventricle	heart
11	chr5:40841000-40842800	Active TSS	GM12878-XiMat	blood
12	chr5:40841200-40842200	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
13	chr5:40841200-40842200	Active TSS	Brain Cingulate Gyrus	brain
14	chr5:40841200-40842200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr5:40841200-40842200	Active TSS	Colonic Mucosa	Colon
16	chr5:40841200-40842200	Active TSS	Fetal Intestine Large	intestine
17	chr5:40841200-40842200	Active TSS	Fetal Kidney	kidney
18	chr5:40841200-40842200	Active TSS	Fetal Muscle Leg	muscle
19	chr5:40841200-40842200	Active TSS	Placenta	Placenta
20	chr5:40841200-40842200	Active TSS	Fetal Stomach	stomach
21	chr5:40841200-40842200	Active TSS	Rectal Mucosa Donor 31	rectum
22	chr5:40841200-40842200	Active TSS	Rectal Smooth Muscle	rectum
23	chr5:40841200-40842200	Active TSS	A549	lung
24	chr5:40841200-40842200	Active TSS	HepG2	liver
25	chr5:40841200-40842400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:40841200-40842400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr5:40841200-40842400	Active TSS	Brain Anterior Caudate	brain
28	chr5:40841200-40842400	Active TSS	Brain Hippocampus Middle	brain
29	chr5:40841200-40842400	Active TSS	Brain Substantia Nigra	brain
30	chr5:40841200-40842400	Active TSS	Ovary	ovary
31	chr5:40841200-40842600	Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr5:40841200-40842800	Active TSS	Stomach Smooth Muscle	stomach
33	chr5:40841200-40842800	Active TSS	NHDF-Ad	bronchial
34	chr5:40841200-40843000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr5:40841200-40843200	Active TSS	Psoas Muscle	Psoas
36	chr5:40841200-40843600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr5:40841200-40844000	Active TSS	Right Atrium	heart
38	chr5:40841400-40842200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr5:40841400-40842200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
40	chr5:40841400-40842200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr5:40841400-40842200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr5:40841400-40842200	Active TSS	Left Ventricle	heart
43	chr5:40841400-40842200	Active TSS	HSMMtube	muscle
44	chr5:40841400-40842400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr5:40841400-40842400	Active TSS	Fetal Intestine Small	intestine
46	chr5:40841400-40842400	Active TSS	NH-A	brain
47	chr5:40841400-40842600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr5:40841400-40842600	Active TSS	Stomach Mucosa	stomach
49	chr5:40841400-40842600	Active TSS	HMEC	breast
50	chr5:40841400-40842600	Active TSS	K562	blood

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