Variant report

Variant	rs57797824
Chromosome Location	chr4:48777317-48777318
allele	C/T
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	chr4:48772120..48774246-chr4:48777185..48779870,3	MCF-7	breast:
4	chr4:48691459..48694072-chr4:48776269..48778861,2	K562	blood:

Variant related genes	Relation type
ENSG00000075539	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10003273	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10008265	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10010571	0.83[ASN][1000 genomes]
rs11727343	0.82[EUR][1000 genomes]
rs11939889	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11943219	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12512637	0.84[EUR][1000 genomes]
rs12641022	0.84[EUR][1000 genomes]
rs13119414	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13141523	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13141838	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13142540	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1517674	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1554256	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1554258	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1589107	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1702798	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1712767	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1980193	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2056201	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2176460	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2354314	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2354937	0.81[AFR][1000 genomes]
rs2354938	0.81[AFR][1000 genomes]
rs2572345	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2572350	0.82[EUR][1000 genomes]
rs2712156	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2712157	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2712158	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2712159	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28733443	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2883561	0.81[AFR][1000 genomes]
rs2883562	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4694906	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4695397	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4695400	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4695401	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62309747	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6447655	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6447660	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6814811	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6830078	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6830848	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6853588	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7657332	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7657698	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7660206	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7665209	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7680280	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7681070	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7697522	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs776588	0.83[AMR][1000 genomes]
rs955683	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9790336	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs57797824	SLC10A4	cis	lung	GTEx
rs57797824	OCIAD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 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	chr4:48759000-48778600	Weak transcription	Fetal Stomach	stomach
3	chr4:48761000-48779800	Weak transcription	Placenta	Placenta
4	chr4:48763000-48779800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr4:48764600-48779800	Weak transcription	HSMM	muscle
6	chr4:48766600-48779800	Weak transcription	Ovary	ovary
7	chr4:48767000-48779800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr4:48768000-48780800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr4:48768600-48780000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr4:48768600-48780800	Weak transcription	Gastric	stomach
11	chr4:48768800-48780000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:48768800-48780000	Weak transcription	Colonic Mucosa	Colon
13	chr4:48769400-48779800	Weak transcription	Pancreas	Pancrea
14	chr4:48769600-48780400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr4:48769800-48777400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr4:48770000-48779800	Weak transcription	Esophagus	oesophagus
17	chr4:48770200-48779400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr4:48770600-48777400	Weak transcription	Fetal Kidney	kidney
19	chr4:48771600-48779000	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr4:48771800-48778400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr4:48772800-48780400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr4:48773000-48779800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr4:48773200-48779800	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr4:48773400-48780400	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr4:48773800-48777600	Enhancers	Primary B cells from cord blood	blood
26	chr4:48773800-48778200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr4:48773800-48779200	Weak transcription	Aorta	Aorta
28	chr4:48773800-48779400	Weak transcription	Hela-S3	cervix
29	chr4:48774200-48777600	Enhancers	Primary T cells fromperipheralblood	blood
30	chr4:48774200-48779200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr4:48774800-48778600	Enhancers	Primary hematopoietic stem cells	blood
32	chr4:48775000-48778400	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr4:48775000-48778400	Weak transcription	Rectal Smooth Muscle	rectum
34	chr4:48775200-48778200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr4:48775400-48778400	Enhancers	NHEK	skin
36	chr4:48775600-48777600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr4:48775600-48777600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr4:48775600-48777800	Enhancers	Left Ventricle	heart
39	chr4:48775800-48778600	Weak transcription	Duodenum Mucosa	Duodenum
40	chr4:48775800-48779000	Weak transcription	NHLF	lung
41	chr4:48776000-48777400	Weak transcription	Fetal Thymus	thymus
42	chr4:48776000-48777600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:48776000-48777600	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr4:48776000-48778200	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr4:48776000-48778200	Weak transcription	HMEC	breast
46	chr4:48776000-48778400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr4:48776000-48778400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr4:48776000-48778400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr4:48776000-48778600	Weak transcription	HUVEC	blood vessel
50	chr4:48776000-48779400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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