Variant report

Variant	rs12409787
Chromosome Location	chr1:212967492-212967493
allele	A/G
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	RCOR1	chr1:212966727-212967493	K562	blood:	n/a	n/a
2	JUN	chr1:212965965-212967572	K562	blood:	n/a	n/a
3	SPI1	chr1:212967439-212968554	GM12878	blood:	n/a	chr1:212968277-212968290 chr1:212968280-212968289 chr1:212968278-212968291
4	NR2F2	chr1:212966334-212968092	K562	blood:	n/a	n/a
5	CBX3	chr1:212966535-212967563	K562	blood:	n/a	n/a
6	ZNF384	chr1:212967464-212968147	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:212965461..212968054-chr1:213031452..213034127,2	MCF-7	breast:
2	chr1:212963881..212969695-chr1:212970420..212976060,10	K562	blood:
3	chr1:212587143..212589756-chr1:212965630..212967810,2	K562	blood:
4	chr1:212965435..212968040-chr1:213139784..213142502,2	K562	blood:
5	chr1:212779632..212786722-chr1:212963640..212968604,10	K562	blood:
6	chr1:212779632..212786722-chr1:212965265..212968763,9	K562	blood:

Variant related genes	Relation type
NSL1	TF binding region
TATDN3	TF binding region
ENSG00000162769	Chromatin interaction
ENSG00000203705	Chromatin interaction
ENSG00000143494	Chromatin interaction
ENSG00000065600	Chromatin interaction
ENSG00000162772	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10863988	0.95[EUR][1000 genomes]
rs11120006	0.96[EUR][1000 genomes]
rs11120010	0.96[EUR][1000 genomes]
rs11120014	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11120018	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11120029	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11120030	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11120035	0.87[ASN][1000 genomes]
rs11120036	0.87[ASN][1000 genomes]
rs11805669	0.83[ASN][1000 genomes]
rs11808846	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12036054	0.87[ASN][1000 genomes]
rs12125867	0.96[EUR][1000 genomes]
rs12128410	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12129465	0.96[EUR][1000 genomes]
rs12129933	0.87[ASN][1000 genomes]
rs12130072	0.87[ASN][1000 genomes]
rs12133124	0.87[ASN][1000 genomes]
rs12133174	0.96[EUR][1000 genomes]
rs12136656	0.87[ASN][1000 genomes]
rs12145131	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12404618	0.96[EUR][1000 genomes]
rs12404885	0.96[EUR][1000 genomes]
rs1507358	0.96[EUR][1000 genomes]
rs17019726	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1857971	0.96[EUR][1000 genomes]
rs2135823	0.96[EUR][1000 genomes]
rs2174781	0.94[EUR][1000 genomes]
rs28872849	0.96[EUR][1000 genomes]
rs3738798	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58203936	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61736926	0.81[EUR][1000 genomes]
rs6540762	0.96[EUR][1000 genomes]
rs6657089	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6664049	0.96[EUR][1000 genomes]
rs6665365	0.93[EUR][1000 genomes]
rs6694190	0.87[ASN][1000 genomes]
rs6702101	0.96[EUR][1000 genomes]
rs73081830	0.96[EUR][1000 genomes]
rs73083705	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73083756	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73083765	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73083778	0.87[ASN][1000 genomes]
rs7515115	0.87[ASN][1000 genomes]
rs7519582	0.92[ASN][1000 genomes]
rs7536456	0.95[EUR][1000 genomes]
rs7548861	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7550288	0.95[EUR][1000 genomes]
rs7552899	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001637	chr1:212907611-213034606	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	esv2756884	chr1:212925429-213006397	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2758997	chr1:212925429-213006397	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1010003	chr1:212944240-212986996	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12409787	FLVCR1	Cis_1M	lymphoblastoid	RTeQTL
rs12409787	TATDN3	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212965800-212971000	Weak transcription	Small Intestine	intestine
2	chr1:212965800-212972000	Weak transcription	Gastric	stomach
3	chr1:212965800-212992600	Weak transcription	Lung	lung
4	chr1:212966000-212967600	Enhancers	Primary B cells from peripheral blood	blood
5	chr1:212966000-212967800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr1:212966000-212968200	Enhancers	Primary T cells fromperipheralblood	blood
7	chr1:212966000-212968400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:212966000-212968400	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr1:212966000-212970200	Weak transcription	Pancreas	Pancrea
10	chr1:212966000-212972000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:212966000-212974800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:212966000-212981200	Weak transcription	Esophagus	oesophagus
13	chr1:212966000-212983000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:212966000-212997400	Weak transcription	Aorta	Aorta
15	chr1:212966200-212967600	Enhancers	Fetal Intestine Small	intestine
16	chr1:212966200-212967800	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr1:212966200-212968000	Enhancers	Fetal Intestine Large	intestine
18	chr1:212966200-212968400	Enhancers	Primary T cells from cord blood	blood
19	chr1:212966200-212968400	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr1:212966200-212969000	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr1:212966200-212970000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr1:212966200-212971000	Weak transcription	HSMMtube	muscle
23	chr1:212966200-212971800	Weak transcription	Fetal Kidney	kidney
24	chr1:212966200-212972000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr1:212966200-212973800	Weak transcription	Colonic Mucosa	Colon
26	chr1:212966200-212975600	Weak transcription	HMEC	breast
27	chr1:212966200-212979800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:212966400-212967800	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr1:212966400-212967800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr1:212966400-212967800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr1:212966400-212967800	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr1:212966400-212967800	Enhancers	Brain Substantia Nigra	brain
33	chr1:212966400-212968000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr1:212966400-212968000	Enhancers	Brain Angular Gyrus	brain
35	chr1:212966400-212968000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:212966400-212968200	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr1:212966400-212968600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:212966400-212968600	Enhancers	HUVEC	blood vessel
39	chr1:212966400-212969000	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr1:212966400-212969000	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr1:212966400-212969000	Weak transcription	Liver	Liver
42	chr1:212966400-212969600	Enhancers	HepG2	liver
43	chr1:212966400-212970000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:212966400-212970000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr1:212966400-212970000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:212966400-212970000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr1:212966400-212970000	Weak transcription	Ovary	ovary
48	chr1:212966400-212970200	Weak transcription	Left Ventricle	heart
49	chr1:212966400-212970200	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr1:212966400-212970400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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