Variant report

Variant	rs62311296
Chromosome Location	chr4:48494101-48494102
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48492886..48494734-chr4:48535449..48537970,2	K562	blood:
2	chr4:48489612..48492154-chr4:48493154..48495602,2	K562	blood:
3	chr4:48478067..48481410-chr4:48493413..48496125,3	K562	blood:

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10018344	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10029732	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10030853	0.88[EUR][1000 genomes]
rs10031777	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10938534	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11734019	0.86[EUR][1000 genomes]
rs11933919	0.88[EUR][1000 genomes]
rs11945562	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12503599	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12506098	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12645501	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13108474	0.86[EUR][1000 genomes]
rs13127730	0.87[EUR][1000 genomes]
rs13138269	0.86[EUR][1000 genomes]
rs13151534	0.80[EUR][1000 genomes]
rs1507862	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1507865	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1702798	0.85[EUR][1000 genomes]
rs1712767	0.83[EUR][1000 genomes]
rs1712768	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1712772	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17575720	0.88[EUR][1000 genomes]
rs17656010	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17656040	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17656076	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17656094	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1876469	0.81[EUR][1000 genomes]
rs2089503	0.87[EUR][1000 genomes]
rs2354348	0.87[EUR][1000 genomes]
rs28470767	0.87[EUR][1000 genomes]
rs28733443	0.83[EUR][1000 genomes]
rs2940324	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2945330	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs3107022	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34558821	0.88[EUR][1000 genomes]
rs34635008	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4536901	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4695391	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59686413	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6447640	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6447645	0.88[EUR][1000 genomes]
rs6447647	0.88[EUR][1000 genomes]
rs6811148	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6819159	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6829144	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6829716	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6830848	0.81[EUR][1000 genomes]
rs6836632	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6838613	0.81[EUR][1000 genomes]
rs6843340	0.84[EUR][1000 genomes]
rs6855022	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6856448	0.88[EUR][1000 genomes]
rs7654770	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7661515	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7678379	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7679210	0.88[EUR][1000 genomes]
rs7683398	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7693461	0.88[EUR][1000 genomes]
rs7697851	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs776584	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs776588	0.82[EUR][1000 genomes]
rs776590	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs776591	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs776601	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs796555	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs937888	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs937889	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs952289	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9884546	0.85[EUR][1000 genomes]
rs992423	0.82[EUR][1000 genomes];0.89[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	nsv879008	chr4:48473439-48496804	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv879009	chr4:48476539-48494546	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62311296	SLC10A4	cis	lung	GTEx
rs62311296	OCIAD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48487200-48505800	Weak transcription	A549	lung
2	chr4:48491400-48494400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr4:48491400-48495400	Weak transcription	K562	blood
4	chr4:48491800-48494200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
5	chr4:48492400-48500800	Weak transcription	Brain Substantia Nigra	brain
6	chr4:48492600-48497800	Weak transcription	Aorta	Aorta
7	chr4:48492600-48510600	Weak transcription	HepG2	liver
8	chr4:48492800-48500200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr4:48492800-48500800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr4:48493000-48494400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
11	chr4:48493200-48494200	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr4:48493400-48494200	ZNF genes & repeats	Lung	lung
13	chr4:48493600-48498000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:48493600-48500800	Weak transcription	Left Ventricle	heart
15	chr4:48493600-48509200	Weak transcription	Pancreas	Pancrea
16	chr4:48493600-48510600	Weak transcription	Gastric	stomach
17	chr4:48493600-48523000	Weak transcription	Right Ventricle	heart
18	chr4:48493800-48494200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
19	chr4:48493800-48494200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
20	chr4:48493800-48494200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
21	chr4:48493800-48498000	Weak transcription	HSMM	muscle
22	chr4:48493800-48499600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr4:48493800-48500800	Weak transcription	Ovary	ovary
24	chr4:48493800-48502800	Weak transcription	Spleen	Spleen
25	chr4:48493800-48509600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr4:48493800-48510600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:48494000-48494400	Bivalent Enhancer	Brain Germinal Matrix	brain
28	chr4:48494000-48499000	Weak transcription	Placenta	Placenta
29	chr4:48494000-48511600	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr4:48494000-48511800	Weak transcription	Colon Smooth Muscle	Colon

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