Variant report

Variant	rs17656010
Chromosome Location	chr4:48541973-48541974
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	chr4:48537925..48542072-chr4:48545238..48547735,4	MCF-7	breast:
2	chr4:48533019..48535101-chr4:48539868..48542141,2	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10018344	0.86[ASN][1000 genomes]
rs10029732	0.85[ASN][1000 genomes]
rs10030853	0.83[ASN][1000 genomes]
rs10031777	0.88[ASN][1000 genomes]
rs10938534	0.91[ASN][1000 genomes]
rs11734019	0.84[ASN][1000 genomes]
rs11933919	0.83[ASN][1000 genomes]
rs12503599	0.87[ASN][1000 genomes]
rs12506098	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12645501	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13127730	0.83[ASN][1000 genomes]
rs13138269	0.84[ASN][1000 genomes]
rs1507862	0.91[ASN][1000 genomes]
rs1507865	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1712768	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1712772	0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs17575720	0.83[ASN][1000 genomes]
rs17656040	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17656076	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17656094	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2089503	0.83[ASN][1000 genomes]
rs2940324	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2945330	0.81[AFR][1000 genomes]
rs3107022	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34558821	0.84[ASN][1000 genomes]
rs34635008	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4536901	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4695391	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59686413	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62311296	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6447640	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6447645	0.84[ASN][1000 genomes]
rs6447647	0.84[ASN][1000 genomes]
rs6811148	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6819159	0.91[ASN][1000 genomes]
rs6829144	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6829716	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6855022	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6856448	0.83[ASN][1000 genomes]
rs7654770	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7661515	0.88[ASN][1000 genomes]
rs7679210	0.84[ASN][1000 genomes]
rs7683398	0.93[ASN][1000 genomes]
rs7693461	0.84[ASN][1000 genomes]
rs776584	0.90[AMR][1000 genomes]
rs776590	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs776591	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs776601	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs796555	0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs937888	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs937889	0.90[AMR][1000 genomes]
rs952289	0.93[ASN][1000 genomes]
rs9884546	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470034	chr4:48427773-48605628	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
2	nsv594121	chr4:48427773-48605628	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv829925	chr4:48467693-48639342	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17656010	SLC10A4	cis	lung	GTEx
rs17656010	OCIAD1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48498600-48593000	Strong transcription	Rectal Mucosa Donor 31	rectum
2	chr4:48499000-48578800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr4:48499000-48589400	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr4:48499600-48581400	Strong transcription	Dnd41	blood
5	chr4:48500200-48588800	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr4:48501400-48578600	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr4:48504400-48575400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:48505200-48575400	Strong transcription	Primary T helper cells PMA-I stimulated	--
9	chr4:48507200-48564000	Strong transcription	Fetal Thymus	thymus
10	chr4:48507600-48568600	Strong transcription	Primary T cells from cord blood	blood
11	chr4:48512200-48542400	Weak transcription	Stomach Mucosa	stomach
12	chr4:48512200-48545000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr4:48515800-48625000	Weak transcription	Hela-S3	cervix
14	chr4:48519400-48566200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr4:48522600-48563200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr4:48524600-48542400	Weak transcription	Psoas Muscle	Psoas
17	chr4:48525000-48544800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr4:48525000-48595600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr4:48525200-48542400	Weak transcription	Right Ventricle	heart
20	chr4:48525200-48543600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr4:48525200-48543600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:48525200-48544800	Weak transcription	Spleen	Spleen
23	chr4:48525200-48552800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr4:48528200-48545200	Weak transcription	HepG2	liver
25	chr4:48528200-48596000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr4:48528800-48543600	Weak transcription	Lung	lung
27	chr4:48529000-48543400	Weak transcription	Fetal Heart	heart
28	chr4:48530400-48542200	Weak transcription	A549	lung
29	chr4:48532200-48542400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr4:48532800-48543200	Weak transcription	Fetal Brain Female	brain
31	chr4:48533000-48542600	Weak transcription	Esophagus	oesophagus
32	chr4:48533000-48545600	Weak transcription	HSMMtube	muscle
33	chr4:48533000-48552600	Weak transcription	Aorta	Aorta
34	chr4:48533400-48542000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr4:48533400-48542400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr4:48533400-48542600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr4:48533400-48542600	Weak transcription	Ovary	ovary
38	chr4:48533400-48543600	Weak transcription	Colon Smooth Muscle	Colon
39	chr4:48533400-48543600	Weak transcription	Gastric	stomach
40	chr4:48533400-48543600	Weak transcription	Pancreas	Pancrea
41	chr4:48533600-48545400	Weak transcription	K562	blood
42	chr4:48533600-48547000	Weak transcription	Fetal Brain Male	brain
43	chr4:48534400-48542600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr4:48535000-48548600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr4:48536400-48542400	Weak transcription	Left Ventricle	heart
46	chr4:48536600-48544000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr4:48536800-48542200	Weak transcription	NHDF-Ad	bronchial
48	chr4:48536800-48543200	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr4:48537400-48542400	Weak transcription	Fetal Kidney	kidney
50	chr4:48538000-48542600	Weak transcription	HMEC	breast

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