Variant report

Variant	rs13142540
Chromosome Location	chr4:48783587-48783588
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	WRNIP1	chr4:48782068-48783638	GM12878	blood:	n/a	n/a
2	FOXA2	chr4:48783563-48783755	HepG2	liver:	n/a	n/a
3	E2F4	chr4:48783510-48783690	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:48564315..48567259-chr4:48782772..48784817,2	K562	blood:
2	chr4:48780694..48783941-chr4:48830567..48835952,11	MCF-7	breast:
3	chr4:48782469..48785403-chr4:48787452..48790375,2	MCF-7	breast:
4	chr4:48783390..48785837-chr4:48789039..48791747,3	K562	blood:
5	chr4:48783503..48785645-chr4:48863021..48865080,2	MCF-7	breast:
6	chr4:48781641..48784567-chr4:48855819..48858602,2	MCF-7	breast:

No data

Variant related genes	Relation type
FRYL	TF binding region
ENSG00000075539	Chromatin interaction
ENSG00000109180	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10003273	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10008265	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10010571	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10049761	0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes]
rs10938537	0.85[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs11727343	0.89[CEU][hapmap];0.86[CHB][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11729065	0.83[EUR][1000 genomes]
rs11733534	0.81[CEU][hapmap];0.91[CHB][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes]
rs11734191	0.81[EUR][1000 genomes]
rs11737677	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs11939889	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11943219	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13113370	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13119041	0.89[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs13119414	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13119504	0.83[AMR][1000 genomes]
rs13141838	0.82[AMR][1000 genomes]
rs13149083	0.85[CEU][hapmap];0.86[CHB][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes]
rs13152270	0.81[EUR][1000 genomes]
rs1517674	0.93[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1554256	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1554258	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1589107	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1876469	0.89[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs1980193	0.83[EUR][1000 genomes]
rs2056201	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2085292	0.89[YRI][hapmap]
rs2102397	0.89[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs2176460	0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2290516	0.88[YRI][hapmap]
rs2354312	0.83[AMR][1000 genomes]
rs2354314	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2354348	0.89[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap]
rs28470767	0.89[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs3761729	0.88[CEU][hapmap];0.86[CHB][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes]
rs4694904	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4694906	0.80[CEU][hapmap]
rs4695400	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4695401	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4695407	0.81[CEU][hapmap];0.91[CHB][hapmap];0.89[YRI][hapmap];0.83[EUR][1000 genomes]
rs57797824	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62310883	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6447651	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6447655	0.80[EUR][1000 genomes]
rs6447666	0.85[YRI][hapmap]
rs6814811	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6818954	0.84[AMR][1000 genomes]
rs6825639	0.87[AMR][1000 genomes]
rs6830078	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6830848	1.00[JPT][hapmap]
rs6843340	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6853588	0.84[ASN][1000 genomes]
rs7654032	0.86[CEU][hapmap];0.87[CHB][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes]
rs7657332	0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7657698	0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7660206	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7667288	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs7670939	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7680280	0.80[EUR][1000 genomes]
rs7681070	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7682859	0.85[AMR][1000 genomes]
rs7697522	0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs776584	1.00[JPT][hapmap]
rs776591	1.00[JPT][hapmap]
rs796555	1.00[JPT][hapmap]
rs9291326	0.85[CEU][hapmap];0.91[CHB][hapmap];0.89[YRI][hapmap];0.83[EUR][1000 genomes]
rs937889	0.95[JPT][hapmap]
rs955683	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9637562	0.83[EUR][1000 genomes]
rs9997920	0.85[CEU][hapmap];0.91[CHB][hapmap];0.89[YRI][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv1793455	chr4:48686817-48859142	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1010381	chr4:48701525-49309842	Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv1003718	chr4:48771947-49083089	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13142540	SLC10A4	cis	lung	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48778800-48783600	Active TSS	Right Ventricle	heart
2	chr4:48779200-48783600	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr4:48779600-48783600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr4:48780000-48783600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr4:48780000-48783600	Active TSS	HSMMtube	muscle
6	chr4:48780000-48783800	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr4:48780200-48783600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr4:48780400-48783800	Active TSS	H9 Cell Line	embryonic stem cell
9	chr4:48780600-48783600	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr4:48780600-48783600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:48780600-48783800	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr4:48780800-48783600	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr4:48780800-48783600	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr4:48780800-48783600	Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr4:48780800-48783600	Active TSS	Rectal Smooth Muscle	rectum
16	chr4:48780800-48783800	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr4:48781000-48783600	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr4:48781000-48783600	Active TSS	Stomach Smooth Muscle	stomach
19	chr4:48781000-48783600	Active TSS	NH-A	brain
20	chr4:48782600-48783600	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr4:48782800-48783600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:48782800-48783600	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr4:48782800-48783600	Flanking Active TSS	HUVEC	blood vessel
24	chr4:48783000-48783600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
25	chr4:48783000-48783600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr4:48783000-48783600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
27	chr4:48783000-48783600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr4:48783000-48783600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr4:48783000-48783600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr4:48783000-48783600	Flanking Active TSS	Fetal Brain Female	brain
31	chr4:48783000-48783600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
32	chr4:48783000-48783600	Flanking Active TSS	Dnd41	blood
33	chr4:48783000-48783600	Flanking Active TSS	HMEC	breast
34	chr4:48783000-48783600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr4:48783000-48783800	Flanking Active TSS	NHEK	skin
36	chr4:48783200-48783600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr4:48783200-48783600	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr4:48783200-48783600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr4:48783200-48783600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr4:48783200-48783600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr4:48783200-48783600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr4:48783200-48783600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
43	chr4:48783200-48783600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr4:48783200-48783600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr4:48783200-48783600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr4:48783200-48783600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr4:48783200-48783600	Flanking Active TSS	Brain Hippocampus Middle	brain
48	chr4:48783200-48783600	Flanking Active TSS	Colonic Mucosa	Colon
49	chr4:48783200-48783600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr4:48783200-48783600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet

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