Variant report

Variant	rs71622283
Chromosome Location	chr5:68593421-68593422
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	chr5:68591369..68594137-chr5:68623717..68625664,2	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10805428	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1134774	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11739602	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11741775	0.87[ASN][1000 genomes]
rs11741826	0.87[ASN][1000 genomes]
rs11742878	0.87[ASN][1000 genomes]
rs11745537	0.87[ASN][1000 genomes]
rs11745591	0.87[ASN][1000 genomes]
rs11957698	0.81[ASN][1000 genomes]
rs12188270	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12189282	0.80[ASN][1000 genomes]
rs12520485	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13154469	0.83[ASN][1000 genomes]
rs13161541	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13163459	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13168973	0.83[ASN][1000 genomes]
rs13178023	0.92[ASN][1000 genomes]
rs13182409	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1976101	0.92[ASN][1000 genomes]
rs2054974	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2054975	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2054976	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2130756	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2172055	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2327638	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2327639	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28499200	0.87[ASN][1000 genomes]
rs2932785	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2932787	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2932788	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2932789	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2932790	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2932793	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2972357	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972364	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2972367	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2972369	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2972379	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2972384	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2972385	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34261117	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34449359	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34591347	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34657177	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34862981	0.83[ASN][1000 genomes]
rs350092	0.93[ASN][1000 genomes]
rs350096	0.94[ASN][1000 genomes]
rs350118	0.89[ASN][1000 genomes]
rs350121	0.86[ASN][1000 genomes]
rs35316810	0.83[ASN][1000 genomes]
rs4288083	0.84[ASN][1000 genomes]
rs4367248	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4423955	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62373182	0.87[ASN][1000 genomes]
rs668139	0.91[ASN][1000 genomes]
rs6865178	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6865481	0.83[ASN][1000 genomes]
rs6869305	0.82[ASN][1000 genomes]
rs6881767	0.83[ASN][1000 genomes]
rs6893648	0.83[ASN][1000 genomes]
rs72767881	0.87[ASN][1000 genomes]
rs7706902	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7711657	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]

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	nsv1018151	chr5:68377118-68667581	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1035004	chr5:68405526-68670101	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs71622283	RAD17	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68531400-68605000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:68541200-68620400	Weak transcription	Stomach Mucosa	stomach
3	chr5:68554200-68604400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr5:68564200-68611200	Weak transcription	Fetal Brain Male	brain
5	chr5:68565600-68627400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr5:68566800-68610800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr5:68575600-68605000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr5:68575600-68608200	Weak transcription	Right Ventricle	heart
9	chr5:68576000-68605200	Weak transcription	Left Ventricle	heart
10	chr5:68576200-68605200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr5:68576200-68609400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr5:68576400-68614400	Weak transcription	Colon Smooth Muscle	Colon
13	chr5:68576400-68627600	Weak transcription	Brain Substantia Nigra	brain
14	chr5:68576400-68627800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr5:68576600-68595400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr5:68576600-68627800	Weak transcription	Brain Angular Gyrus	brain
17	chr5:68577200-68601400	Weak transcription	Aorta	Aorta
18	chr5:68577400-68594400	Weak transcription	Esophagus	oesophagus
19	chr5:68577400-68605200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr5:68577400-68607800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr5:68577400-68628200	Weak transcription	Small Intestine	intestine
22	chr5:68577600-68619800	Weak transcription	Fetal Muscle Trunk	muscle
23	chr5:68577600-68627400	Weak transcription	NHEK	skin
24	chr5:68577800-68626600	Weak transcription	A549	lung
25	chr5:68579000-68603600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr5:68580600-68594200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr5:68581600-68601200	Weak transcription	Fetal Thymus	thymus
28	chr5:68581600-68627600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr5:68581800-68593600	Weak transcription	Pancreas	Pancrea
30	chr5:68581800-68594200	Weak transcription	Adipose Nuclei	Adipose
31	chr5:68581800-68594400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr5:68581800-68605200	Weak transcription	GM12878-XiMat	blood
33	chr5:68581800-68608200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr5:68581800-68609000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr5:68581800-68609200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr5:68581800-68611000	Weak transcription	Psoas Muscle	Psoas
37	chr5:68581800-68617800	Weak transcription	Brain Hippocampus Middle	brain
38	chr5:68581800-68626800	Weak transcription	Fetal Brain Female	brain
39	chr5:68581800-68627600	Weak transcription	Brain Anterior Caudate	brain
40	chr5:68582000-68601600	Weak transcription	Fetal Muscle Leg	muscle
41	chr5:68582800-68622400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr5:68585000-68594200	Weak transcription	Gastric	stomach
43	chr5:68585000-68609000	Weak transcription	Spleen	Spleen
44	chr5:68586000-68594200	Weak transcription	Primary hematopoietic stem cells	blood
45	chr5:68587200-68602400	Strong transcription	Fetal Intestine Small	intestine
46	chr5:68587600-68597800	Strong transcription	Liver	Liver
47	chr5:68587800-68597800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr5:68588400-68595600	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr5:68588600-68593600	Weak transcription	Lung	lung
50	chr5:68588600-68595600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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