Variant report

Variant	rs12261146
Chromosome Location	chr10:50021541-50021542
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:49998728..50000233-chr10:50020617..50022326,2	MCF-7	breast:
2	chr10:50018526..50021577-chr10:50026027..50031410,4	MCF-7	breast:
3	chr10:50016415..50019036-chr10:50020234..50023570,4	MCF-7	breast:
4	chr10:50012510..50015290-chr10:50020965..50023375,3	MCF-7	breast:
5	chr10:50000720..50003091-chr10:50019887..50021986,2	MCF-7	breast:
6	chr10:50021104..50023943-chr10:50032685..50035174,2	MCF-7	breast:
7	chr10:50009310..50017840-chr10:50018505..50026491,17	MCF-7	breast:
8	chr10:50019507..50021681-chr10:50026930..50029178,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000128815	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11101512	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11101516	0.96[EUR][1000 genomes]
rs11101518	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs11101519	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];0.98[EUR][1000 genomes]
rs11101520	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs11101521	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs11101522	0.98[EUR][1000 genomes]
rs11101524	0.98[EUR][1000 genomes]
rs11101525	0.98[EUR][1000 genomes]
rs11101526	0.98[EUR][1000 genomes]
rs11101527	0.98[EUR][1000 genomes]
rs11101528	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];0.98[EUR][1000 genomes]
rs12246033	0.98[EUR][1000 genomes]
rs12247830	1.00[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes]
rs12247839	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];0.98[EUR][1000 genomes]
rs12248218	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs12249974	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];0.98[EUR][1000 genomes]
rs12251517	1.00[CEU][hapmap];0.85[JPT][hapmap];0.95[EUR][1000 genomes]
rs12260555	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs12264889	0.98[EUR][1000 genomes]
rs12268007	1.00[CEU][hapmap];0.84[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12268803	0.98[EUR][1000 genomes]
rs17699445	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs17699451	1.00[CEU][hapmap];0.92[CHB][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs17836512	0.88[JPT][hapmap]
rs2377655	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2928402	0.84[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2928403	0.84[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3750864	0.88[JPT][hapmap]
rs41283275	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs45520233	0.98[EUR][1000 genomes]
rs4596990	0.96[EUR][1000 genomes]
rs61838883	0.98[EUR][1000 genomes]
rs61838884	0.98[EUR][1000 genomes]
rs61838885	0.98[EUR][1000 genomes]
rs6537578	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes]
rs6537579	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs7918931	0.84[CHB][hapmap];0.88[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	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv831865	chr10:49994254-50164239	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12261146	ZNF488	cis	cerebellum	SCAN
rs12261146	WDFY4	cis	Lymphoblastoid	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50005200-50026800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:50009600-50028000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr10:50013200-50023800	Strong transcription	GM12878-XiMat	blood
4	chr10:50013600-50028200	Strong transcription	Primary B cells from peripheral blood	blood
5	chr10:50013600-50061000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr10:50014200-50030000	Weak transcription	Right Atrium	heart
7	chr10:50014600-50021800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr10:50015000-50023000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr10:50015200-50063400	Strong transcription	Primary B cells from cord blood	blood
10	chr10:50015600-50023200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr10:50015600-50029800	Weak transcription	Gastric	stomach
12	chr10:50016200-50063000	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr10:50016200-50063000	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr10:50016600-50022800	Strong transcription	Spleen	Spleen
15	chr10:50016600-50062400	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr10:50017000-50022600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr10:50017600-50023600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr10:50017800-50022000	Weak transcription	Lung	lung
19	chr10:50019400-50029000	Weak transcription	Primary T cells from cord blood	blood
20	chr10:50020000-50052000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr10:50020200-50022800	Weak transcription	NHEK	skin
22	chr10:50020200-50023200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr10:50020400-50022600	Enhancers	Fetal Muscle Leg	muscle
24	chr10:50020600-50022200	Enhancers	Adipose Nuclei	Adipose
25	chr10:50020800-50021800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr10:50020800-50022200	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr10:50020800-50022400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr10:50020800-50022600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr10:50021000-50022000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr10:50021000-50022200	Enhancers	Fetal Stomach	stomach
31	chr10:50021000-50022800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr10:50021200-50021600	Weak transcription	Fetal Muscle Trunk	muscle
33	chr10:50021200-50021600	Weak transcription	Left Ventricle	heart
34	chr10:50021200-50027800	Weak transcription	Fetal Thymus	thymus

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