Variant report

Variant	rs2056201
Chromosome Location	chr4:48776829-48776830
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48768871..48771023-chr4:48775443..48777643,2	MCF-7	breast:
2	chr4:48774500..48780275-chr4:48780685..48784374,5	MCF-7	breast:
3	chr4:48772504..48776956-chr4:48777763..48782974,9	K562	blood:
4	chr4:48691459..48694072-chr4:48776269..48778861,2	K562	blood:

Variant related genes	Relation type
ENSG00000075539	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10003273	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10008265	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10010571	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10049761	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11727343	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11729065	0.80[ASN][1000 genomes]
rs11939889	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11943219	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13113370	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13119414	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13119504	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13142540	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13149083	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1517674	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1554256	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1554258	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1589107	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1980193	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2176460	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2354312	0.83[AMR][1000 genomes]
rs2354314	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3761729	0.80[ASN][1000 genomes]
rs4694904	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4695397	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4695400	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4695401	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4695407	0.81[ASN][1000 genomes]
rs57797824	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62310883	0.80[EUR][1000 genomes]
rs6447651	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6447655	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6447660	0.81[ASN][1000 genomes]
rs6814811	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6818954	0.84[AMR][1000 genomes]
rs6825639	0.81[AMR][1000 genomes]
rs6830078	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6853588	0.84[ASN][1000 genomes]
rs7654032	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7657332	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7657698	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7660206	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7670939	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7680280	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7681070	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7682859	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7697522	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9291326	0.80[ASN][1000 genomes]
rs955683	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9790336	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9997920	0.81[ASN][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
rs2056201	SLC10A4	cis	lung	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48731600-48779800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:48747200-48777200	Weak transcription	Fetal Intestine Small	intestine
3	chr4:48751600-48777200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:48759000-48778600	Weak transcription	Fetal Stomach	stomach
5	chr4:48761000-48779800	Weak transcription	Placenta	Placenta
6	chr4:48762000-48777200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr4:48763000-48779800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr4:48764600-48779800	Weak transcription	HSMM	muscle
9	chr4:48766600-48779800	Weak transcription	Ovary	ovary
10	chr4:48767000-48779800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr4:48768000-48780800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr4:48768600-48777200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:48768600-48777200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr4:48768600-48780000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr4:48768600-48780800	Weak transcription	Gastric	stomach
16	chr4:48768800-48777200	Weak transcription	Fetal Intestine Large	intestine
17	chr4:48768800-48780000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr4:48768800-48780000	Weak transcription	Colonic Mucosa	Colon
19	chr4:48769400-48779800	Weak transcription	Pancreas	Pancrea
20	chr4:48769600-48780400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr4:48769800-48777000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr4:48769800-48777000	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr4:48769800-48777000	Weak transcription	Brain Anterior Caudate	brain
24	chr4:48769800-48777400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr4:48770000-48779800	Weak transcription	Esophagus	oesophagus
26	chr4:48770200-48777000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr4:48770200-48777000	Weak transcription	K562	blood
28	chr4:48770200-48777200	Weak transcription	Brain Germinal Matrix	brain
29	chr4:48770200-48779400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr4:48770600-48777400	Weak transcription	Fetal Kidney	kidney
31	chr4:48771600-48779000	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr4:48771800-48778400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr4:48772800-48780400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr4:48773000-48779800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr4:48773200-48779800	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr4:48773400-48780400	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr4:48773600-48777200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr4:48773800-48777200	Weak transcription	Right Ventricle	heart
39	chr4:48773800-48777600	Enhancers	Primary B cells from cord blood	blood
40	chr4:48773800-48778200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr4:48773800-48779200	Weak transcription	Aorta	Aorta
42	chr4:48773800-48779400	Weak transcription	Hela-S3	cervix
43	chr4:48774000-48777200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr4:48774200-48777600	Enhancers	Primary T cells fromperipheralblood	blood
45	chr4:48774200-48779200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr4:48774800-48778600	Enhancers	Primary hematopoietic stem cells	blood
47	chr4:48775000-48778400	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr4:48775000-48778400	Weak transcription	Rectal Smooth Muscle	rectum
49	chr4:48775200-48778200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr4:48775400-48777000	Weak transcription	Brain Hippocampus Middle	brain

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