Variant report

Variant	rs2666428
Chromosome Location	chr1:226589709-226589710
allele	C/T
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:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:226570760..226578039-chr1:226587444..226591845,7	K562	blood:
2	chr1:226588622..226590477-chr1:226592586..226594961,2	MCF-7	breast:
3	chr1:226589383..226591665-chr1:226794295..226796050,2	K562	blood:
4	chr1:226496219..226498371-chr1:226587979..226589846,3	K562	blood:
5	chr1:226570760..226572399-chr1:226587444..226589965,2	K562	blood:
6	chr1:226549481..226552453-chr1:226589185..226592308,3	K562	blood:
7	chr1:226309303..226311386-chr1:226588616..226590233,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143799	Chromatin interaction
ENSG00000183814	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1104893	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11801168	0.91[JPT][hapmap]
rs12567614	0.89[GIH][hapmap];1.00[JPT][hapmap]
rs1341333	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1341335	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1341336	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1397550	0.89[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1417765	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805414	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1828445	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1828446	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1858548	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1858549	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1858550	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1865220	0.96[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1865221	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1865222	0.96[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2027439	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2048424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2048426	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2136875	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2249844	0.89[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2377313	0.80[AMR][1000 genomes]
rs2570368	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2570369	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2570370	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2666427	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2695235	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2695236	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2695237	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2695238	0.85[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2695239	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2695240	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2793376	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2793377	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2793378	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2793380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2793382	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2793654	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2793655	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2793657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3219090	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3219110	0.93[LWK][hapmap];0.83[MKK][hapmap];0.85[YRI][hapmap]
rs3219112	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3219119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3754376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6677172	1.00[JPT][hapmap]
rs747657	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs907186	0.92[JPT][hapmap]
rs9426568	0.84[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv832770	chr1:226465130-226655512	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv832781	chr1:226570901-226750697	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226543000-226590800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr1:226543000-226590800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:226543000-226591400	Strong transcription	Primary T cells from cord blood	blood
4	chr1:226543400-226590200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr1:226543400-226591400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:226543600-226590400	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr1:226543600-226591400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr1:226544200-226590400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr1:226544600-226591800	Strong transcription	Dnd41	blood
10	chr1:226544800-226590800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:226545000-226590800	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr1:226545400-226590600	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:226546200-226590600	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr1:226557200-226590600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:226557400-226590200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:226558400-226590200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:226563000-226591400	Weak transcription	Stomach Mucosa	stomach
18	chr1:226564200-226590600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr1:226568800-226591400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:226578600-226592200	Weak transcription	Small Intestine	intestine
21	chr1:226580600-226590400	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr1:226580800-226590800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:226581800-226589800	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr1:226581800-226590600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:226581800-226591600	Strong transcription	Fetal Intestine Small	intestine
26	chr1:226583400-226590800	Strong transcription	Fetal Stomach	stomach
27	chr1:226584200-226590200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:226584200-226590600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:226584400-226590200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr1:226584400-226590400	Strong transcription	Primary hematopoietic stem cells	blood
31	chr1:226584400-226590600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:226584600-226590000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr1:226584600-226590000	Strong transcription	A549	lung
34	chr1:226584800-226589800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr1:226584800-226590600	Strong transcription	Duodenum Mucosa	Duodenum
36	chr1:226585000-226590400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr1:226585000-226590800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr1:226585200-226590400	Strong transcription	Fetal Brain Female	brain
39	chr1:226585200-226590600	Strong transcription	Fetal Thymus	thymus
40	chr1:226585200-226590800	Strong transcription	Hela-S3	cervix
41	chr1:226585400-226590400	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr1:226585600-226589800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr1:226585600-226590600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr1:226586000-226590000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:226586000-226590800	Strong transcription	Fetal Lung	lung
46	chr1:226586200-226589800	Weak transcription	Right Atrium	heart
47	chr1:226586200-226590000	Strong transcription	Fetal Intestine Large	intestine
48	chr1:226586400-226589800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
49	chr1:226586400-226590000	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr1:226586400-226590000	Strong transcription	Colonic Mucosa	Colon

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