Variant report

Variant	rs2292231
Chromosome Location	chr4:48505177-48505178
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48504789..48507033-chr4:48508012..48511920,5	K562	blood:
2	chr4:48484114..48487251-chr4:48504187..48509460,5	K562	blood:
3	chr4:48147874..48150153-chr4:48505108..48507497,2	K562	blood:
4	chr4:48504140..48506911-chr4:48507772..48510124,3	K562	blood:

Variant related genes	Relation type
ENSG00000145248	Chromatin interaction
ENSG00000135605	Chromatin interaction
ENSG00000075539	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10018344	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10029732	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10030853	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10031777	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10049761	1.00[CEU][hapmap];0.85[YRI][hapmap]
rs10938534	1.00[CEU][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10938537	0.96[CEU][hapmap];0.83[AMR][1000 genomes]
rs11728565	0.85[AMR][1000 genomes]
rs11734019	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11737677	0.96[CEU][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes]
rs11933919	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11945562	1.00[CEU][hapmap];0.91[AMR][1000 genomes]
rs12503599	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12645501	0.81[ASN][1000 genomes]
rs13108474	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13119041	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs13127730	0.82[EUR][1000 genomes]
rs13138269	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13151534	0.84[AMR][1000 genomes]
rs1507862	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17575720	1.00[CEU][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17656040	0.81[CEU][hapmap]
rs1876469	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs2089503	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2102397	1.00[CEU][hapmap]
rs2354348	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28470767	1.00[CEU][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34558821	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6447645	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6447647	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6811148	0.81[ASN][1000 genomes]
rs6819159	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6836632	1.00[CEU][hapmap];0.88[AMR][1000 genomes]
rs6843340	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs6856448	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7661515	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7667288	0.96[CEU][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes]
rs7678379	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7679210	1.00[CEU][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7683398	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7693461	0.96[CEU][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7697851	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs952289	0.93[CEU][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9884546	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs992423	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2292231	SLC10A4	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48487200-48505800	Weak transcription	A549	lung
2	chr4:48492600-48510600	Weak transcription	HepG2	liver
3	chr4:48493600-48509200	Weak transcription	Pancreas	Pancrea
4	chr4:48493600-48510600	Weak transcription	Gastric	stomach
5	chr4:48493600-48523000	Weak transcription	Right Ventricle	heart
6	chr4:48493800-48509600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr4:48493800-48510600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:48494000-48511600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr4:48494000-48511800	Weak transcription	Colon Smooth Muscle	Colon
10	chr4:48494200-48509800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:48494200-48510600	Weak transcription	HSMMtube	muscle
12	chr4:48494800-48509400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr4:48494800-48510600	Weak transcription	Esophagus	oesophagus
14	chr4:48495000-48510000	Weak transcription	Brain Germinal Matrix	brain
15	chr4:48495200-48513600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr4:48495400-48523000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr4:48495600-48509600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr4:48495600-48509800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:48495800-48511600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr4:48496000-48506200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr4:48496200-48540600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr4:48496400-48510600	Weak transcription	Small Intestine	intestine
23	chr4:48496800-48511400	Weak transcription	Fetal Heart	heart
24	chr4:48497000-48507600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr4:48497000-48521600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr4:48497200-48507800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr4:48497600-48509200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr4:48497800-48509200	Weak transcription	Psoas Muscle	Psoas
29	chr4:48498000-48507800	Weak transcription	Lung	lung
30	chr4:48498200-48539600	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr4:48498200-48540000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr4:48498400-48509800	Weak transcription	Aorta	Aorta
33	chr4:48498400-48511600	Weak transcription	Stomach Mucosa	stomach
34	chr4:48498400-48511800	Weak transcription	Fetal Brain Male	brain
35	chr4:48498600-48593000	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr4:48499000-48510600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr4:48499000-48578800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr4:48499000-48589400	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr4:48499200-48540000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr4:48499400-48527400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr4:48499600-48581400	Strong transcription	Dnd41	blood
42	chr4:48499800-48505600	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr4:48499800-48506200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr4:48499800-48506600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr4:48499800-48511600	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr4:48499800-48540000	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr4:48500200-48517400	Strong transcription	Primary B cells from peripheral blood	blood
48	chr4:48500200-48588800	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr4:48500400-48540000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr4:48501000-48538800	Strong transcription	Primary neutrophils fromperipheralblood	blood

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