Variant report

Variant	rs73309977
Chromosome Location	chr12:49721122-49721123
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:49721089-49721483	K562	blood:	n/a	n/a
2	POLR2A	chr12:49720523-49721466	SK-N-MC	brain:	n/a	n/a
3	GATA3	chr12:49721096-49721546	MCF-7	breast:	n/a	chr12:49721297-49721304 chr12:49721292-49721304
4	POLR2A	chr12:49720922-49721378	K562	blood:	n/a	n/a
5	POLR2A	chr12:49719207-49721909	K562	blood:	n/a	n/a
6	POLR2A	chr12:49720637-49721124	PFSK-1	brain:	n/a	n/a
7	NR2F2	chr12:49721041-49721564	HepG2	liver:	n/a	n/a
8	POLR2A	chr12:49720941-49721414	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:49719939..49721986-chr12:49744313..49747277,2	K562	blood:
2	chr12:49658793..49660553-chr12:49719371..49721124,2	MCF-7	breast:
3	chr12:49715312..49722303-chr12:49739075..49744198,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258334	TF binding region
ENSG00000178401	Chromatin interaction
ENSG00000167553	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10400435	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10400567	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11168973	0.93[ASN][1000 genomes]
rs11168974	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11168975	0.96[ASN][1000 genomes]
rs11503617	0.93[ASN][1000 genomes]
rs11835303	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12313488	0.93[ASN][1000 genomes]
rs12580931	0.89[ASN][1000 genomes]
rs12822293	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2070760	0.89[ASN][1000 genomes]
rs28493849	0.89[ASN][1000 genomes]
rs3088008	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4243545	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4898504	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4898519	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57241318	0.96[ASN][1000 genomes]
rs59575791	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67236923	0.89[ASN][1000 genomes]
rs67309388	0.89[ASN][1000 genomes]
rs73112143	0.89[ASN][1000 genomes]
rs7488343	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
5	nsv1042122	chr12:49678529-49823168	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
6	nsv1039176	chr12:49678529-49832618	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
7	nsv899068	chr12:49714103-49924637	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv832405	chr12:49720279-49910862	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs73309977	C1QL4	cis	Thyroid	GTEx

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49717400-49726800	Weak transcription	Right Atrium	heart
2	chr12:49717600-49723000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr12:49717600-49725000	Weak transcription	Pancreas	Pancrea
4	chr12:49717800-49722600	Weak transcription	Fetal Intestine Large	intestine
5	chr12:49717800-49727000	Weak transcription	Esophagus	oesophagus
6	chr12:49718000-49721400	Strong transcription	A549	lung
7	chr12:49718000-49722600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr12:49718000-49722800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:49718000-49724600	Weak transcription	Spleen	Spleen
10	chr12:49718000-49724800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:49718000-49725000	Weak transcription	Colonic Mucosa	Colon
12	chr12:49718000-49725000	Weak transcription	Fetal Heart	heart
13	chr12:49718000-49725000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr12:49718000-49725200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:49718000-49725200	Weak transcription	Duodenum Mucosa	Duodenum
16	chr12:49718000-49725200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr12:49718000-49725400	Weak transcription	Placenta	Placenta
18	chr12:49718000-49726200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr12:49718000-49726400	Weak transcription	Primary B cells from cord blood	blood
20	chr12:49718000-49730200	Weak transcription	Gastric	stomach
21	chr12:49718200-49724400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:49718200-49725200	Weak transcription	Fetal Brain Female	brain
23	chr12:49718200-49725400	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr12:49718200-49725600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:49718200-49725600	Weak transcription	Fetal Kidney	kidney
26	chr12:49718400-49721200	Strong transcription	Hela-S3	cervix
27	chr12:49718400-49722800	Weak transcription	Brain Germinal Matrix	brain
28	chr12:49718400-49723800	Weak transcription	Fetal Lung	lung
29	chr12:49718400-49724200	Strong transcription	K562	blood
30	chr12:49718400-49724800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr12:49718400-49724800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr12:49718600-49725000	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr12:49718600-49725400	Strong transcription	NHEK	skin
34	chr12:49718600-49725600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:49718800-49721800	Strong transcription	HUVEC	blood vessel
36	chr12:49719000-49724600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr12:49719200-49721400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr12:49719200-49721400	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr12:49719200-49722400	Strong transcription	Primary hematopoietic stem cells	blood
40	chr12:49719200-49723800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr12:49719200-49724000	Strong transcription	Fetal Stomach	stomach
42	chr12:49719200-49724200	Strong transcription	Fetal Muscle Trunk	muscle
43	chr12:49719200-49724400	Strong transcription	HepG2	liver
44	chr12:49719200-49724600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr12:49719200-49724600	Strong transcription	Fetal Muscle Leg	muscle
46	chr12:49719200-49724800	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr12:49719200-49725000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr12:49719200-49725000	Strong transcription	Fetal Intestine Small	intestine
49	chr12:49719200-49725200	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr12:49719200-49725200	Strong transcription	HUES48 Cell Line	embryonic stem cell

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