Variant report

Variant	rs2928402
Chromosome Location	chr10:50018165-50018166
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:50011096..50015039-chr10:50015649..50020097,7	MCF-7	breast:
2	chr10:49972674..49975169-chr10:50017821..50020027,2	MCF-7	breast:
3	chr10:50016415..50019036-chr10:50020234..50023570,4	MCF-7	breast:
4	chr10:50011301..50013130-chr10:50016318..50018256,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11101512	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11101516	0.82[ASN][1000 genomes]
rs11101518	0.84[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.94[TSI][hapmap];0.81[ASN][1000 genomes]
rs11101519	0.84[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs11101520	0.84[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.94[TSI][hapmap];0.81[ASN][1000 genomes]
rs11101521	0.84[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.94[TSI][hapmap];0.81[ASN][1000 genomes]
rs11101522	0.82[ASN][1000 genomes]
rs11101524	0.81[ASN][1000 genomes]
rs11101525	0.81[ASN][1000 genomes]
rs11101526	0.81[ASN][1000 genomes]
rs11101527	0.81[ASN][1000 genomes]
rs11101528	0.84[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs12246033	0.84[ASN][1000 genomes]
rs12247830	0.84[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs12247839	0.84[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap]
rs12248218	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs12249974	0.84[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap]
rs12251517	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs12260555	0.84[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.94[TSI][hapmap];0.82[ASN][1000 genomes]
rs12261146	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]
rs12268007	0.84[CEU][hapmap];0.92[CHB][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12268803	0.82[ASN][1000 genomes]
rs17699445	0.84[CEU][hapmap]
rs17699451	0.84[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[TSI][hapmap];0.82[ASN][1000 genomes]
rs17836512	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs2377655	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2928403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3750864	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs41283275	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs45520233	0.82[ASN][1000 genomes]
rs4596990	0.81[ASN][1000 genomes]
rs61838883	0.81[ASN][1000 genomes]
rs61838884	0.81[ASN][1000 genomes]
rs61838885	0.81[ASN][1000 genomes]
rs6537578	0.83[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6537579	0.84[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.94[TSI][hapmap];0.81[ASN][1000 genomes]
rs7918931	0.92[CHB][hapmap];0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	esv3446258	chr10:50015246-50019644	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2928402	WDFY4	cis	Lymphoblastoid	GTEx
rs2928402	ZNF488	cis	cerebellum	SCAN

Chromatin state (count:36 , 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	chr10:50014600-50019400	Weak transcription	Brain Substantia Nigra	brain
8	chr10:50014600-50019800	Weak transcription	Left Ventricle	heart
9	chr10:50014600-50020800	Strong transcription	Primary hematopoietic stem cells	blood
10	chr10:50014600-50021800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr10:50014800-50018600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr10:50014800-50019600	Weak transcription	NHLF	lung
13	chr10:50014800-50020600	Weak transcription	Adipose Nuclei	Adipose
14	chr10:50014800-50020800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr10:50014800-50020800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr10:50015000-50018400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr10:50015000-50023000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr10:50015200-50063400	Strong transcription	Primary B cells from cord blood	blood
19	chr10:50015600-50023200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr10:50015600-50029800	Weak transcription	Gastric	stomach
21	chr10:50016200-50063000	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr10:50016200-50063000	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr10:50016400-50019000	Weak transcription	Aorta	Aorta
24	chr10:50016600-50018800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr10:50016600-50019000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr10:50016600-50019600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr10:50016600-50022800	Strong transcription	Spleen	Spleen
28	chr10:50016600-50062400	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr10:50016800-50018800	Weak transcription	Primary T cells from cord blood	blood
30	chr10:50016800-50019000	Weak transcription	NHEK	skin
31	chr10:50017000-50019800	Weak transcription	Fetal Muscle Leg	muscle
32	chr10:50017000-50022600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr10:50017600-50023600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr10:50017800-50018400	Weak transcription	Pancreas	Pancrea
35	chr10:50017800-50022000	Weak transcription	Lung	lung
36	chr10:50018000-50019400	Weak transcription	Rectal Mucosa Donor 29	rectum

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