Variant report

Variant	rs2127590
Chromosome Location	chr10:50013594-50013595
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:50007868..50011089-chr10:50011494..50014036,4	MCF-7	breast:
2	chr10:50012510..50015290-chr10:50020965..50023375,3	MCF-7	breast:
3	chr10:50012639..50013621-chr10:50022857..50023759,3	MCF-7	breast:
4	chr10:50011032..50014812-chr10:50025927..50027937,3	K562	blood:
5	chr10:50011096..50015039-chr10:50015649..50020097,7	MCF-7	breast:
6	chr10:50012503..50014685-chr10:50027009..50029930,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128815	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10776647	0.89[JPT][hapmap]
rs10776648	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs10857655	0.89[JPT][hapmap]
rs11101511	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs11101529	0.89[JPT][hapmap]
rs11101530	0.89[JPT][hapmap]
rs11101531	0.88[JPT][hapmap]
rs1904596	0.89[JPT][hapmap]
rs1904603	0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs2002588	0.89[JPT][hapmap]
rs2170132	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2448539	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs2448540	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2448545	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs2457214	0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs2620888	0.93[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap]
rs2620889	0.82[JPT][hapmap]
rs2620891	0.89[JPT][hapmap]
rs2620896	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2620898	0.89[JPT][hapmap]
rs2620903	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2620904	0.89[JPT][hapmap]
rs2663031	0.90[LWK][hapmap]
rs2663035	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2663044	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2663053	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2928393	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2928401	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2940704	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2943244	0.89[JPT][hapmap]
rs2947344	0.90[LWK][hapmap];0.82[TSI][hapmap]
rs2947345	0.90[LWK][hapmap];0.82[TSI][hapmap]
rs3747872	0.89[JPT][hapmap]
rs3747874	0.89[JPT][hapmap]
rs3747875	0.89[JPT][hapmap]
rs3860188	0.89[JPT][hapmap]
rs4838648	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6537576	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6537580	0.84[CHB][hapmap]
rs7079766	0.89[JPT][hapmap]
rs726786	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7900138	0.89[JPT][hapmap]
rs7913005	0.89[JPT][hapmap]
rs877819	0.89[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2127590	WDFY4	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50005200-50026800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:50007200-50014600	Weak transcription	NHLF	lung
3	chr10:50007200-50017200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr10:50008200-50013600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr10:50008200-50015000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr10:50008400-50013600	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr10:50009000-50013600	Genic enhancers	Primary B cells from peripheral blood	blood
8	chr10:50009200-50015200	Genic enhancers	Primary B cells from cord blood	blood
9	chr10:50009600-50014800	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr10:50009600-50028000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr10:50010800-50014800	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr10:50010800-50016000	Enhancers	Fetal Thymus	thymus
13	chr10:50011000-50014000	Enhancers	Fetal Brain Male	brain
14	chr10:50011000-50014600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr10:50011200-50014800	Enhancers	Brain Germinal Matrix	brain
16	chr10:50011200-50015400	Enhancers	Fetal Muscle Leg	muscle
17	chr10:50011200-50016600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
18	chr10:50011400-50016200	Genic enhancers	Primary monocytes fromperipheralblood	blood
19	chr10:50011600-50013800	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr10:50011600-50016200	Genic enhancers	Monocytes-CD14+_RO01746	blood
21	chr10:50011600-50017000	Enhancers	Fetal Stomach	stomach
22	chr10:50011800-50014600	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr10:50012000-50013600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr10:50012000-50014800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr10:50012000-50014800	Enhancers	Fetal Lung	lung
26	chr10:50012200-50013600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr10:50012200-50014200	Enhancers	Brain Cingulate Gyrus	brain
28	chr10:50012200-50014600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr10:50012400-50014600	Flanking Active TSS	Primary T cells from cord blood	blood
30	chr10:50012400-50014600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr10:50012600-50013800	Enhancers	Primary hematopoietic stem cells	blood
32	chr10:50012600-50014600	Enhancers	Fetal Intestine Large	intestine
33	chr10:50012600-50014600	Enhancers	Left Ventricle	heart
34	chr10:50012600-50015000	Enhancers	Fetal Muscle Trunk	muscle
35	chr10:50012800-50013600	Enhancers	Right Ventricle	heart
36	chr10:50012800-50013800	Enhancers	Adipose Nuclei	Adipose
37	chr10:50012800-50014000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr10:50012800-50014000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr10:50012800-50014400	Enhancers	Fetal Heart	heart
40	chr10:50012800-50014600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr10:50012800-50014800	Enhancers	Brain Angular Gyrus	brain
42	chr10:50012800-50016600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr10:50012800-50016800	Enhancers	NHEK	skin
44	chr10:50013000-50013800	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr10:50013000-50014200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr10:50013000-50014200	Enhancers	Right Atrium	heart
47	chr10:50013000-50014600	Enhancers	Fetal Brain Female	brain
48	chr10:50013000-50014600	Enhancers	Fetal Intestine Small	intestine
49	chr10:50013000-50014800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
50	chr10:50013000-50014800	Enhancers	Lung	lung

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