Variant report

Variant	rs2242378
Chromosome Location	chr4:125632581-125632582
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:125630101..125632893-chr4:125662563..125664427,2	K562	blood:
2	chr4:125355738..125360405-chr4:125631320..125634850,4	MCF-7	breast:
3	chr4:125601250..125602938-chr4:125631120..125633142,2	K562	blood:
4	chr4:125631616..125633726-chr4:125883727..125886839,4	MCF-7	breast:
5	chr4:125600002..125602938-chr4:125630037..125632620,2	K562	blood:
6	chr4:125252420..125254567-chr4:125631458..125633343,2	MCF-7	breast:
7	chr4:125587788..125590476-chr4:125631233..125632777,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248506	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10006577	0.85[ASN][1000 genomes]
rs10006893	0.85[CHB][hapmap];0.92[MEX][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10013174	0.82[ASN][1000 genomes]
rs10018651	0.85[ASN][1000 genomes]
rs10028864	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1015968	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1016382	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs1016383	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10518442	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12331436	0.82[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13104292	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13107141	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13110120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13110982	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13117832	0.85[ASN][1000 genomes]
rs13130626	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13144437	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13150707	0.91[ASN][1000 genomes]
rs1472290	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1495126	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1495127	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1498024	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17008475	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17008478	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1874748	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1995135	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2036204	0.86[CHB][hapmap];0.82[CHD][hapmap];0.92[MEX][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs220738	0.85[ASN][1000 genomes]
rs28399027	0.87[ASN][1000 genomes]
rs3172524	0.92[CHB][hapmap];0.82[CHD][hapmap];0.92[MEX][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs34348208	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34748024	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34877613	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35053443	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35180555	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35282937	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35333384	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35463553	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35958270	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36177260	0.85[ASN][1000 genomes]
rs3733471	0.85[ASN][1000 genomes]
rs4833999	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4834000	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56902532	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59841071	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6534448	0.85[ASN][1000 genomes]
rs6815682	0.91[ASN][1000 genomes]
rs6816263	0.92[CHB][hapmap];0.84[JPT][hapmap];0.97[ASN][1000 genomes]
rs6849375	0.91[ASN][1000 genomes]
rs6849813	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9307543	0.85[ASN][1000 genomes]
rs9307544	0.85[ASN][1000 genomes]
rs9999425	0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3343011	chr4:125632527-125635375	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2242378	ANKRD50	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:125622400-125632600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:125625600-125633000	Weak transcription	Small Intestine	intestine
3	chr4:125629200-125632800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr4:125629600-125632600	Enhancers	HepG2	liver
5	chr4:125629600-125633400	Active TSS	Right Atrium	heart
6	chr4:125630000-125634800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr4:125630200-125632600	Enhancers	Liver	Liver
8	chr4:125630400-125632600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr4:125630600-125635000	Active TSS	A549	lung
10	chr4:125630600-125635200	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr4:125630800-125633400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr4:125631000-125632600	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr4:125631000-125632600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr4:125631000-125633000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:125631000-125633200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr4:125631000-125633200	Flanking Active TSS	Dnd41	blood
17	chr4:125631000-125634200	Active TSS	Placenta	Placenta
18	chr4:125631200-125633200	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr4:125631200-125633200	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr4:125631200-125634600	Active TSS	Brain Cingulate Gyrus	brain
21	chr4:125631400-125632600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr4:125631400-125632600	Enhancers	Primary B cells from cord blood	blood
23	chr4:125631400-125634600	Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr4:125631600-125632600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr4:125631600-125632600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr4:125631600-125632600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr4:125631600-125632600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
28	chr4:125631600-125632600	Active TSS	Duodenum Mucosa	Duodenum
29	chr4:125631600-125632600	Weak transcription	Pancreas	Pancrea
30	chr4:125631600-125632600	Active TSS	Rectal Mucosa Donor 31	rectum
31	chr4:125631600-125632600	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr4:125631600-125632800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
33	chr4:125631600-125633000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr4:125631600-125634200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:125631600-125634200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:125631600-125634400	Active TSS	H1 Cell Line	embryonic stem cell
37	chr4:125631600-125634400	Active TSS	Fetal Brain Female	brain
38	chr4:125631600-125634600	Active TSS	Fetal Muscle Trunk	muscle
39	chr4:125631600-125634600	Active TSS	Fetal Muscle Leg	muscle
40	chr4:125631600-125634600	Active TSS	Gastric	stomach
41	chr4:125631600-125634600	Active TSS	Lung	lung
42	chr4:125631600-125634600	Active TSS	NHLF	lung
43	chr4:125631600-125634800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr4:125631600-125634800	Active TSS	Aorta	Aorta
45	chr4:125631600-125634800	Active TSS	Ovary	ovary
46	chr4:125631600-125634800	Active TSS	Right Ventricle	heart
47	chr4:125631800-125632600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
48	chr4:125631800-125633000	Weak transcription	Spleen	Spleen
49	chr4:125631800-125634200	Active TSS	NHDF-Ad	bronchial
50	chr4:125631800-125634400	Active TSS	Fetal Intestine Small	intestine

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