Variant report

Variant	rs1043975
Chromosome Location	chr4:53732611-53732612
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:53728327..53731010-chr4:53731656..53733511,2	MCF-7	breast:
2	chr4:53731855..53733936-chr4:53741528..53744311,2	MCF-7	breast:
3	chr4:53727120..53730074-chr4:53731609..53733512,4	K562	blood:

Variant related genes	Relation type
ENSG00000128045	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10000595	0.86[TSI][hapmap]
rs10001855	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10008073	0.86[CEU][hapmap];0.93[CHB][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10014464	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10026175	0.89[CEU][hapmap]
rs10028567	0.89[CEU][hapmap];0.92[TSI][hapmap]
rs1047959	0.89[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs10866413	0.93[JPT][hapmap]
rs11930907	0.91[ASN][1000 genomes]
rs11934293	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11941562	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1483685	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1483686	0.89[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs1483687	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17082081	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17082143	0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17082147	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17613967	0.84[TSI][hapmap]
rs17643154	1.00[TSI][hapmap]
rs1963003	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2003198	0.91[ASN][1000 genomes]
rs2017237	0.84[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2046364	0.92[ASN][1000 genomes]
rs2062253	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2200226	0.95[ASN][1000 genomes]
rs2279334	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306601	0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2411259	0.80[CEU][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs2411281	0.90[ASN][1000 genomes]
rs28419463	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28454903	0.81[EUR][1000 genomes]
rs28489424	0.81[EUR][1000 genomes]
rs28526700	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28704139	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28733375	0.84[EUR][1000 genomes]
rs28735908	0.81[EUR][1000 genomes]
rs28811693	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2898681	0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.90[ASN][1000 genomes]
rs301119	0.86[JPT][hapmap]
rs301123	0.84[CHB][hapmap];0.93[JPT][hapmap];0.92[TSI][hapmap]
rs301135	0.86[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes]
rs301136	0.80[AMR][1000 genomes]
rs4242020	0.81[EUR][1000 genomes]
rs4309903	0.81[EUR][1000 genomes]
rs4864673	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4864679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4864681	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4864682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4864683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4864688	0.92[ASN][1000 genomes]
rs4864690	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4864691	0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4865422	0.81[EUR][1000 genomes]
rs4990628	0.81[EUR][1000 genomes]
rs5012592	0.89[CEU][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs59649036	0.92[ASN][1000 genomes]
rs61268502	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62336785	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62336788	0.97[EUR][1000 genomes]
rs62336791	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62336792	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62336794	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62336795	0.93[ASN][1000 genomes]
rs62336823	0.88[ASN][1000 genomes]
rs62338801	0.81[EUR][1000 genomes]
rs62338805	0.81[EUR][1000 genomes]
rs6833096	0.91[ASN][1000 genomes]
rs6839084	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6852148	0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs73143042	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs900607	0.94[ASN][1000 genomes]
rs922932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs922933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9646	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9993034	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][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	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1004086	chr4:53698581-53773183	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	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
rs1043975	SGCB	cis	lymphoblastoid	seeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53728800-53738400	Weak transcription	Small Intestine	intestine
2	chr4:53729200-53734200	Weak transcription	Psoas Muscle	Psoas
3	chr4:53729200-53734400	Weak transcription	HSMMtube	muscle
4	chr4:53729200-53735200	Weak transcription	Colonic Mucosa	Colon
5	chr4:53729200-53751200	Weak transcription	GM12878-XiMat	blood
6	chr4:53729200-53807800	Weak transcription	Esophagus	oesophagus
7	chr4:53729400-53734000	Weak transcription	Brain Anterior Caudate	brain
8	chr4:53729400-53738600	Weak transcription	HMEC	breast
9	chr4:53729400-53739200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:53729400-53743200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr4:53729400-53752400	Weak transcription	Primary B cells from cord blood	blood
12	chr4:53729400-53753800	Weak transcription	Duodenum Mucosa	Duodenum
13	chr4:53729600-53732800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr4:53729600-53733400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:53729600-53733800	Weak transcription	NHEK	skin
16	chr4:53729600-53734000	Weak transcription	Brain Angular Gyrus	brain
17	chr4:53729600-53735200	Weak transcription	NHDF-Ad	bronchial
18	chr4:53729600-53739400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:53729600-53739600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr4:53729600-53742200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr4:53729800-53734400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr4:53729800-53737000	Weak transcription	Primary T cells from cord blood	blood
23	chr4:53729800-53739400	Weak transcription	Fetal Intestine Large	intestine
24	chr4:53730000-53733600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:53730000-53743800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr4:53730200-53734600	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr4:53730200-53736600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr4:53730600-53732800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr4:53730800-53733600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr4:53731000-53735400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr4:53731200-53733400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr4:53731200-53736000	Enhancers	Right Atrium	heart
33	chr4:53731400-53732800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr4:53731400-53733600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr4:53731400-53734200	Weak transcription	Brain Hippocampus Middle	brain
36	chr4:53731400-53734400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr4:53731400-53734400	Weak transcription	Brain Substantia Nigra	brain
38	chr4:53731400-53751000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr4:53731600-53732800	Strong transcription	Fetal Intestine Small	intestine
40	chr4:53731600-53734000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr4:53731600-53734400	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
42	chr4:53731600-53736200	Weak transcription	Stomach Mucosa	stomach
43	chr4:53731600-53739400	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr4:53731800-53732800	Genic enhancers	Fetal Lung	lung
45	chr4:53731800-53734200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr4:53731800-53736600	Weak transcription	Colon Smooth Muscle	Colon
47	chr4:53731800-53738000	Weak transcription	Liver	Liver
48	chr4:53732000-53733400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
49	chr4:53732000-53733800	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr4:53732000-53733800	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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