Variant report

Variant	rs2012451
Chromosome Location	chr22:31844373-31844374
allele	G/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	chr22:31843500-31844690	K562	blood:	n/a	n/a
2	POLR2A	chr22:31843645-31844451	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	22:31836635-31847259..22:31936958-31958600	GM12878	blood:
2	22:31836635-31847259..22:32529813-32538538	K562	blood:
3	chr22:31836012..31838119-chr22:31842804..31844542,2	MCF-7	breast:
4	chr22:31840511..31842559-chr22:31842977..31844692,2	MCF-7	breast:
5	22:31836635-31847259..22:32284948-32287956	Hela-S3	cervix:

Variant related genes	Relation type
EIF4ENIF1	TF binding region
ENSG00000214093	Chromatin interaction
ENSG00000232707	Chromatin interaction
ENSG00000239674	Chromatin interaction
ENSG00000227813	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs12166373	0.86[MEX][hapmap];0.80[TSI][hapmap]
rs13053245	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs131209	0.86[MEX][hapmap];0.80[TSI][hapmap]
rs131213	0.86[MEX][hapmap];0.80[TSI][hapmap]
rs1543416	0.85[LWK][hapmap]
rs1916	0.81[CEU][hapmap];0.82[CHB][hapmap];0.83[LWK][hapmap];0.86[MKK][hapmap];0.82[YRI][hapmap]
rs2006771	0.81[CEU][hapmap]
rs2103853	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs28715	0.86[MEX][hapmap]
rs35143518	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4541328	0.83[EUR][1000 genomes]
rs4820045	0.86[MEX][hapmap];0.87[TSI][hapmap]
rs4820048	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4820961	0.82[MEX][hapmap];0.80[TSI][hapmap]
rs4820969	0.86[YRI][hapmap]
rs4820974	0.92[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4820983	0.80[LWK][hapmap]
rs5753625	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs5753630	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs5994397	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs5997929	0.82[MEX][hapmap];0.80[TSI][hapmap]
rs5997971	0.96[YRI][hapmap]
rs5997980	0.85[AFR][1000 genomes]
rs5997981	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs5997986	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs5997988	0.94[ASW][hapmap];0.96[CEU][hapmap];0.90[GIH][hapmap];0.95[LWK][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5997989	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5997990	0.93[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs5998002	0.81[CEU][hapmap];0.82[CHB][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5998003	0.83[EUR][1000 genomes]
rs5998004	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5998012	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5998017	0.81[EUR][1000 genomes]
rs5998021	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs6518745	0.83[ASW][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs7287402	0.81[MEX][hapmap];0.80[TSI][hapmap]
rs7287937	0.81[CEU][hapmap]
rs7289941	0.81[CEU][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs739427	0.80[TSI][hapmap]
rs926928	0.88[ASW][hapmap];0.92[LWK][hapmap];0.81[MEX][hapmap];0.95[MKK][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9609263	0.87[MEX][hapmap]
rs9621255	0.84[AFR][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	nsv834176	chr22:31682426-31864701	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	nsv1063634	chr22:31797004-31921254	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
3	nsv459872	chr22:31833759-31977594	Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
4	nsv588894	chr22:31833759-31977594	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2012451	CRYBB1	cis	cerebellum	SCAN
rs2012451	MN1	cis	parietal	SCAN
rs2012451	LIMK2	cis	cerebellum	SCAN
rs2012451	DRG1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31797000-31884400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr22:31797000-31884400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr22:31797200-31845400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr22:31797200-31846200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr22:31797200-31846400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr22:31797200-31860600	Strong transcription	Fetal Stomach	stomach
7	chr22:31797400-31846800	Strong transcription	Duodenum Mucosa	Duodenum
8	chr22:31797800-31844800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr22:31797800-31846800	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr22:31799000-31845400	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr22:31799200-31846600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr22:31803600-31844600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr22:31804600-31847000	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr22:31805000-31844800	Strong transcription	Primary B cells from peripheral blood	blood
15	chr22:31805600-31844800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr22:31813600-31845000	Strong transcription	Fetal Thymus	thymus
17	chr22:31814000-31846400	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr22:31814200-31846800	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr22:31814400-31845600	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr22:31814400-31845800	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr22:31814400-31846800	Strong transcription	Fetal Intestine Large	intestine
22	chr22:31814800-31844600	Strong transcription	Thymus	Thymus
23	chr22:31814800-31846600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr22:31815000-31844600	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr22:31815000-31846600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr22:31815000-31846800	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr22:31815000-31868200	Strong transcription	Dnd41	blood
28	chr22:31815000-31883400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr22:31815400-31844400	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr22:31815400-31844400	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr22:31815400-31846200	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr22:31815400-31846600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr22:31815400-31846600	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr22:31821000-31844600	Strong transcription	Primary B cells from cord blood	blood
35	chr22:31821000-31845000	Strong transcription	Primary T cells from cord blood	blood
36	chr22:31821200-31844600	Strong transcription	Fetal Brain Female	brain
37	chr22:31822200-31846600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr22:31822400-31859800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr22:31823600-31884600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr22:31826600-31846400	Strong transcription	Brain Germinal Matrix	brain
41	chr22:31827200-31846600	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr22:31827600-31846600	Strong transcription	Osteobl	bone
43	chr22:31828800-31845000	Strong transcription	NHLF	lung
44	chr22:31828800-31845600	Strong transcription	GM12878-XiMat	blood
45	chr22:31829000-31844800	Strong transcription	Primary hematopoietic stem cells	blood
46	chr22:31829400-31844400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr22:31829600-31846400	Strong transcription	Brain Substantia Nigra	brain
48	chr22:31829600-31852000	Strong transcription	Stomach Smooth Muscle	stomach
49	chr22:31829800-31846600	Strong transcription	HSMM	muscle
50	chr22:31831200-31850000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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