Variant report

Variant	rs6865178
Chromosome Location	chr5:68569957-68569958
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:68562809..68566315-chr5:68569480..68571051,3	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs100192	0.86[CHB][hapmap]
rs10805428	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1134774	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11739602	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12188270	0.85[AFR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12520485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13161541	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13163459	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13178023	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13182409	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs163443	0.85[CHB][hapmap]
rs164386	0.82[CHB][hapmap]
rs164390	0.86[CHB][hapmap]
rs1976101	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[GIH][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs2054974	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2054975	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2054976	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2130756	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2172055	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2327638	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2327639	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2932785	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2932787	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2932788	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2932789	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2932790	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2932793	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2972357	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2972364	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2972367	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2972369	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2972379	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2972384	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2972385	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34261117	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34449359	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34591347	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34657177	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs350092	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs350096	0.87[EUR][1000 genomes]
rs350107	0.82[CHB][hapmap]
rs350118	0.85[EUR][1000 genomes]
rs350121	0.85[EUR][1000 genomes]
rs352626	0.86[CHB][hapmap]
rs389686	0.81[CHB][hapmap]
rs4367248	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4423955	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs444305	0.82[CHB][hapmap]
rs4976159	0.80[ASN][1000 genomes]
rs4976188	0.81[ASN][1000 genomes]
rs648489	0.82[CHB][hapmap]
rs668139	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6862253	0.81[ASN][1000 genomes]
rs71622283	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7706902	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7711657	0.92[EUR][1000 genomes]
rs875459	0.86[CHB][hapmap]

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	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
3	nsv965550	chr5:68556472-68572197	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6865178	RAD17	cis	Muscle Skeletal	GTEx
rs6865178	MRPS36	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68531200-68584200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:68531400-68605000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:68532400-68574600	Weak transcription	Spleen	Spleen
4	chr5:68533200-68576800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr5:68534400-68575200	Weak transcription	Aorta	Aorta
6	chr5:68541200-68620400	Weak transcription	Stomach Mucosa	stomach
7	chr5:68546200-68579200	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr5:68549400-68577600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr5:68549600-68577600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr5:68550400-68581800	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr5:68550600-68577000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:68551800-68570200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr5:68552000-68581200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr5:68552200-68580800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr5:68552200-68588000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr5:68553000-68581400	Weak transcription	Psoas Muscle	Psoas
17	chr5:68553800-68575800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr5:68553800-68587800	Weak transcription	Colonic Mucosa	Colon
19	chr5:68554000-68577600	Weak transcription	Fetal Heart	heart
20	chr5:68554200-68604400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr5:68556200-68574800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr5:68557200-68572400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr5:68557200-68575400	Weak transcription	Gastric	stomach
24	chr5:68557400-68575200	Weak transcription	Pancreas	Pancrea
25	chr5:68557400-68575400	Weak transcription	Right Ventricle	heart
26	chr5:68559000-68583400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr5:68559200-68581200	Weak transcription	Fetal Kidney	kidney
28	chr5:68559600-68584000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr5:68559800-68571600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr5:68559800-68574200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr5:68560000-68572200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr5:68560400-68575400	Weak transcription	HSMMtube	muscle
33	chr5:68560600-68572000	Weak transcription	Brain Hippocampus Middle	brain
34	chr5:68560600-68574600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr5:68562000-68576400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr5:68562400-68577000	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr5:68562600-68570200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr5:68562600-68575000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr5:68562600-68578800	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr5:68562600-68584200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr5:68562800-68577400	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr5:68563000-68585200	Strong transcription	Liver	Liver
43	chr5:68563200-68577400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr5:68563400-68576000	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr5:68564200-68573600	Weak transcription	Left Ventricle	heart
46	chr5:68564200-68575400	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr5:68564200-68575400	Weak transcription	Esophagus	oesophagus
48	chr5:68564200-68611200	Weak transcription	Fetal Brain Male	brain
49	chr5:68564400-68575400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr5:68565400-68573600	Weak transcription	Ovary	ovary

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