Variant report

Variant	rs1004243
Chromosome Location	chr22:31497879-31497880
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:31497058..31499268-chr22:31535389..31537818,2	MCF-7	breast:
2	chr22:31478816..31484481-chr22:31493390..31497944,7	MCF-7	breast:
3	chr22:31476077..31485695-chr22:31490616..31506508,29	K562	blood:
4	chr22:31494012..31497911-chr22:31499689..31503512,5	K562	blood:

Variant related genes	Relation type
ENSG00000100078	Chromatin interaction
ENSG00000198832	Chromatin interaction
ENSG00000183963	Chromatin interaction
ENSG00000273387	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11089487	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11089488	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11089489	0.84[AFR][1000 genomes]
rs11703403	0.91[AFR][1000 genomes]
rs11703478	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11705137	0.95[LWK][hapmap];0.88[MKK][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes]
rs12167220	0.95[LWK][hapmap];0.88[MKK][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes]
rs12330010	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12484046	0.91[CEU][hapmap]
rs13053329	0.88[AFR][1000 genomes]
rs13054770	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1558023	0.87[CEU][hapmap]
rs1807739	0.86[AFR][1000 genomes]
rs35657209	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs35685997	0.86[AMR][1000 genomes]
rs4281997	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820934	0.83[CEU][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes]
rs4820938	0.86[YRI][hapmap];0.80[AFR][1000 genomes]
rs4820939	0.82[AFR][1000 genomes]
rs4820940	0.91[YRI][hapmap];0.86[AFR][1000 genomes]
rs4820941	0.86[AFR][1000 genomes]
rs7284108	0.83[AMR][1000 genomes]
rs7284757	0.87[CEU][hapmap];0.86[GIH][hapmap];0.89[MEX][hapmap]
rs7285617	0.83[CEU][hapmap]
rs737930	0.87[CEU][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes]
rs740231	0.84[GIH][hapmap]
rs8135353	0.87[CEU][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs9619163	0.87[CEU][hapmap]
rs9621173	0.83[AMR][1000 genomes]
rs9621184	0.86[ASW][hapmap];0.91[CEU][hapmap];0.93[GIH][hapmap];0.93[LWK][hapmap];0.89[MEX][hapmap];0.82[MKK][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9621185	0.91[CEU][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9621187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9621188	0.95[LWK][hapmap];0.88[MKK][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9896	chr22:31369204-31513933	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv829173	chr22:31450043-31543956	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv914975	chr22:31466083-31514477	Active TSS Flanking Active TSS Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv914976	chr22:31475307-31543260	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv914977	chr22:31477563-31514477	Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1004243	CRYBB1	cis	cerebellum	SCAN
rs1004243	CCDC117	cis	parietal	SCAN
rs1004243	CHEK2	cis	cerebellum	SCAN
rs1004243	SELM	cis	parietal	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31482000-31500800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr22:31482000-31501000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr22:31482000-31501200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr22:31482200-31498800	Strong transcription	Fetal Lung	lung
5	chr22:31483000-31498600	Strong transcription	Thymus	Thymus
6	chr22:31483200-31500600	Strong transcription	HUVEC	blood vessel
7	chr22:31483200-31502000	Strong transcription	NHEK	skin
8	chr22:31483800-31499600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr22:31484000-31498600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr22:31484000-31502600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr22:31484400-31499200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr22:31485200-31500800	Weak transcription	Fetal Thymus	thymus
13	chr22:31485200-31503000	Weak transcription	Fetal Kidney	kidney
14	chr22:31485400-31498000	Strong transcription	Adipose Nuclei	Adipose
15	chr22:31485400-31500000	Strong transcription	Pancreas	Pancrea
16	chr22:31485800-31502800	Weak transcription	GM12878-XiMat	blood
17	chr22:31486800-31498600	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr22:31488400-31500400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr22:31489000-31500000	Weak transcription	Primary T cells from cord blood	blood
20	chr22:31489200-31498200	Weak transcription	A549	lung
21	chr22:31489200-31501400	Strong transcription	Gastric	stomach
22	chr22:31489600-31501600	Weak transcription	Brain Angular Gyrus	brain
23	chr22:31490400-31498400	Weak transcription	Right Atrium	heart
24	chr22:31490800-31500200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr22:31490800-31502000	Weak transcription	Brain Substantia Nigra	brain
26	chr22:31491000-31500600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
27	chr22:31491400-31502000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
28	chr22:31491800-31498400	Strong transcription	Lung	lung
29	chr22:31491800-31502600	Weak transcription	Liver	Liver
30	chr22:31493000-31500800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr22:31493200-31498200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr22:31493600-31498000	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr22:31493800-31498200	Weak transcription	Brain Hippocampus Middle	brain
34	chr22:31493800-31499800	Genic enhancers	NHDF-Ad	bronchial
35	chr22:31493800-31501800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr22:31494800-31498000	Weak transcription	Psoas Muscle	Psoas
37	chr22:31494800-31498400	Weak transcription	Stomach Mucosa	stomach
38	chr22:31494800-31499000	Strong transcription	Duodenum Mucosa	Duodenum
39	chr22:31494800-31499400	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr22:31494800-31500000	Genic enhancers	Rectal Smooth Muscle	rectum
41	chr22:31494800-31501600	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr22:31495200-31498400	Strong transcription	Brain Germinal Matrix	brain
43	chr22:31495200-31498400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr22:31495200-31498800	Strong transcription	Fetal Muscle Trunk	muscle
45	chr22:31495200-31499000	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr22:31495200-31500000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr22:31495200-31501800	Strong transcription	Left Ventricle	heart
48	chr22:31495400-31498000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr22:31495400-31498000	Weak transcription	K562	blood
50	chr22:31495400-31498200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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