Variant report

Variant	rs301123
Chromosome Location	chr4:53796814-53796815
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:53794290..53797029-chr4:53800788..53802475,2	MCF-7	breast:
2	chr4:53795070..53797861-chr4:53805518..53809319,3	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10001855	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10008073	0.85[CHB][hapmap]
rs10028567	0.85[TSI][hapmap]
rs1043975	0.84[CHB][hapmap];0.93[JPT][hapmap];0.92[TSI][hapmap]
rs1047959	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs10866413	0.89[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs1483686	0.92[TSI][hapmap]
rs17082143	0.93[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17082147	0.94[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes]
rs17643154	0.87[CEU][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs2017237	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs2062253	0.84[CHB][hapmap];0.93[JPT][hapmap];0.92[TSI][hapmap]
rs2279334	0.84[CHB][hapmap];0.93[JPT][hapmap];0.92[TSI][hapmap]
rs2306601	0.89[CHB][hapmap];0.93[JPT][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2411259	0.92[TSI][hapmap]
rs2898681	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs301095	0.93[AFR][1000 genomes]
rs301097	0.92[YRI][hapmap];0.93[AFR][1000 genomes]
rs301115	0.92[ASW][hapmap];0.82[YRI][hapmap]
rs301117	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs301118	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs301119	0.94[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs301120	0.94[ASN][1000 genomes]
rs301121	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301122	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs301124	0.95[ASN][1000 genomes]
rs301125	0.95[AFR][1000 genomes]
rs301126	0.97[LWK][hapmap];0.95[MKK][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes]
rs301131	0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs301135	1.00[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.92[TSI][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs301136	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs448567	1.00[YRI][hapmap]
rs4864679	0.84[CHB][hapmap];0.93[JPT][hapmap];0.92[TSI][hapmap]
rs4864682	0.84[CHB][hapmap];0.93[JPT][hapmap];0.92[TSI][hapmap]
rs4864683	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs4864690	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs4864691	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs5012592	0.92[TSI][hapmap]
rs6839084	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs6852148	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs90020	0.92[ASW][hapmap];0.95[LWK][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs900607	0.80[AMR][1000 genomes]
rs922932	0.84[CHB][hapmap];0.93[JPT][hapmap];0.92[TSI][hapmap]
rs922933	0.84[CHB][hapmap];0.93[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs301123	SGCB	cis	lymphoblastoid	seeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53729200-53807800	Weak transcription	Esophagus	oesophagus
2	chr4:53734600-53822400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr4:53768800-53815600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr4:53769000-53804400	Weak transcription	Primary B cells from peripheral blood	blood
5	chr4:53774600-53798400	Weak transcription	HSMMtube	muscle
6	chr4:53782200-53799000	Weak transcription	NHLF	lung
7	chr4:53782400-53797200	Weak transcription	Liver	Liver
8	chr4:53785600-53798400	Weak transcription	NHDF-Ad	bronchial
9	chr4:53786600-53861400	Weak transcription	Primary B cells from cord blood	blood
10	chr4:53786800-53799000	Weak transcription	Primary T cells from cord blood	blood
11	chr4:53790200-53799400	Weak transcription	Left Ventricle	heart
12	chr4:53792200-53798600	Weak transcription	NH-A	brain
13	chr4:53792200-53798800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:53792200-53799000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:53792600-53797200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr4:53792600-53797200	Weak transcription	Stomach Mucosa	stomach
17	chr4:53792600-53797600	Weak transcription	Fetal Muscle Leg	muscle
18	chr4:53793000-53797200	Weak transcription	Fetal Intestine Large	intestine
19	chr4:53793000-53797200	Weak transcription	Fetal Intestine Small	intestine
20	chr4:53793000-53797200	Weak transcription	Pancreas	Pancrea
21	chr4:53793000-53797600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr4:53793000-53797600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr4:53793000-53797600	Weak transcription	Gastric	stomach
24	chr4:53793000-53798800	Weak transcription	Fetal Lung	lung
25	chr4:53793000-53799000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:53793000-53799000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr4:53793000-53805600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr4:53793200-53797200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr4:53794000-53797200	Weak transcription	Fetal Heart	heart
30	chr4:53794000-53798800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr4:53794800-53797400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr4:53795200-53797800	Weak transcription	Psoas Muscle	Psoas
33	chr4:53795800-53797000	Weak transcription	Colon Smooth Muscle	Colon
34	chr4:53795800-53798800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:53796000-53800400	Weak transcription	Placenta	Placenta
36	chr4:53796400-53809800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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