Variant report

Variant	rs6584128
Chromosome Location	chr10:99171926-99171927
allele	G/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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:99165782..99177128-chr10:99179856..99189832,30	MCF-7	breast:
2	chr10:99170419..99173744-chr10:99178891..99183198,3	MCF-7	breast:
3	chr10:99159566..99161975-chr10:99171116..99175343,4	K562	blood:
4	chr10:99168511..99173804-chr10:99184850..99187816,7	MCF-7	breast:
5	chr10:99166045..99168504-chr10:99170322..99173005,2	K562	blood:
6	chr10:99160204..99163024-chr10:99171580..99174293,2	K562	blood:
7	chr10:99171315..99175453-chr10:99176654..99180468,6	K562	blood:
8	chr10:99171445..99174170-chr10:99204178..99207806,5	MCF-7	breast:
9	chr10:99163386..99166099-chr10:99171495..99174383,2	MCF-7	breast:
10	chr10:99166892..99169975-chr10:99170359..99172836,3	MCF-7	breast:
11	chr10:99170047..99172632-chr10:99208471..99210539,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000200737	Chromatin interaction
ENSG00000224474	Chromatin interaction
ENSG00000052749	Chromatin interaction
ENSG00000171314	Chromatin interaction
ENSG00000171307	Chromatin interaction
ENSG00000231970	Chromatin interaction
ENSG00000171311	Chromatin interaction

Extended variants
information (count: 121 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10444013	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10444014	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10444016	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1048442	0.95[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1048445	0.85[CHD][hapmap]
rs10786336	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10786337	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10786338	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10786339	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10786340	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10786341	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10786342	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10786343	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10786344	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10786345	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10786346	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10786347	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10882903	0.83[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10882904	0.87[CEU][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs10882907	0.86[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs10882908	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10882909	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10882910	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10882911	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10882912	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10882913	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10882914	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10882915	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10882916	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10882917	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10882922	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10882924	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10882926	0.95[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10882929	0.84[AMR][1000 genomes]
rs10882930	0.84[AMR][1000 genomes]
rs10882931	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10882934	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11189144	0.81[EUR][1000 genomes]
rs11189165	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs11189168	0.87[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs11189172	0.95[CEU][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs11189173	0.82[CEU][hapmap]
rs11189174	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11189175	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11189177	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11189178	0.90[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11189179	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11189180	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11189181	0.84[EUR][1000 genomes]
rs11189182	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11189183	0.87[EUR][1000 genomes]
rs11189191	0.90[EUR][1000 genomes]
rs11189192	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11189195	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11189196	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11189197	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11189200	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11189204	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11189206	1.00[CEU][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11189208	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11812223	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11814021	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11817852	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11817875	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12258560	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12266723	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12359257	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs1537645	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1537646	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17112674	0.87[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.80[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17112676	0.85[EUR][1000 genomes]
rs1810983	0.83[EUR][1000 genomes]
rs1932001	0.83[CEU][hapmap];0.87[GIH][hapmap];0.81[AMR][1000 genomes]
rs2275089	0.95[CEU][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2275090	0.95[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2275581	0.88[CHD][hapmap]
rs2297667	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2297668	0.95[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2297988	0.87[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs3737194	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3814553	0.95[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3818787	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3818908	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4635018	0.95[CEU][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60237341	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61861912	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61863813	0.80[EUR][1000 genomes]
rs61863815	0.85[EUR][1000 genomes]
rs61863819	0.88[EUR][1000 genomes]
rs6584126	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6584127	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7074511	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7078004	0.95[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7078782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7084654	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7088410	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7092350	0.95[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7092499	0.95[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7096801	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7895695	0.91[CEU][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7896100	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7903562	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7909345	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7916665	0.80[AMR][1000 genomes]
rs7918742	0.82[EUR][1000 genomes]
rs7921585	0.83[EUR][1000 genomes]
rs7922512	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7923385	0.83[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs869967	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs954149	0.87[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs9787426	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9787454	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9887991	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9887994	0.80[AMR][1000 genomes]
rs9888026	0.95[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9888116	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9888117	0.95[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv467438	chr10:99126249-99173870	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv552024	chr10:99126249-99173870	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv467440	chr10:99134784-99204791	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv552025	chr10:99134784-99204791	Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs6584128	FRAT1	cis	multi-tissue	Pritchard
rs6584128	RP11-452K12.7	cis	Whole Blood	GTEx
rs6584128	RRP12	cis	Heart Left Ventricle	GTEx
rs6584128	MMS19	cis	cerebellum	SCAN
rs6584128	RRP12	cis	Muscle Skeletal	GTEx
rs6584128	RRP12	cis	cerebellum	SCAN
rs6584128	MMS19	cis	parietal	SCAN
rs6584128	KIAA0690	cis	multi-tissue	Pritchard
rs6584128	FRAT2	cis	multi-tissue	Pritchard
rs6584128	RRP12	cis	parietal	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99161600-99178800	Weak transcription	Fetal Stomach	stomach
2	chr10:99161600-99185200	Weak transcription	Pancreas	Pancrea
3	chr10:99167400-99172400	Weak transcription	Primary T cells from cord blood	blood
4	chr10:99167400-99174000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr10:99167400-99174800	Weak transcription	NHDF-Ad	bronchial
6	chr10:99167400-99176200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr10:99167400-99178000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr10:99167400-99179000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr10:99167400-99185200	Weak transcription	Fetal Lung	lung
10	chr10:99167400-99185400	Weak transcription	Gastric	stomach
11	chr10:99167600-99172400	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr10:99167600-99172400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr10:99167600-99172400	Weak transcription	GM12878-XiMat	blood
14	chr10:99167600-99172600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr10:99167600-99172600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr10:99167600-99172600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr10:99167600-99172600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr10:99167600-99172600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr10:99167600-99172600	Weak transcription	Fetal Thymus	thymus
20	chr10:99167600-99172800	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr10:99167600-99172800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr10:99167600-99172800	Weak transcription	Thymus	Thymus
23	chr10:99167600-99172800	Weak transcription	HUVEC	blood vessel
24	chr10:99167600-99173400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr10:99167600-99173400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr10:99167600-99173400	Weak transcription	Esophagus	oesophagus
27	chr10:99167600-99173600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr10:99167600-99173600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr10:99167600-99174800	Weak transcription	Brain Anterior Caudate	brain
30	chr10:99167600-99177800	Weak transcription	Fetal Intestine Large	intestine
31	chr10:99167600-99178000	Weak transcription	Fetal Muscle Leg	muscle
32	chr10:99167600-99178400	Weak transcription	Right Atrium	heart
33	chr10:99167600-99185200	Weak transcription	Fetal Intestine Small	intestine
34	chr10:99167600-99185200	Weak transcription	Left Ventricle	heart
35	chr10:99167800-99172400	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr10:99167800-99172600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr10:99167800-99172600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr10:99167800-99173400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr10:99167800-99178000	Weak transcription	A549	lung
40	chr10:99168000-99173400	Weak transcription	Primary hematopoietic stem cells	blood
41	chr10:99168800-99172200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr10:99168800-99172200	Weak transcription	HMEC	breast
43	chr10:99168800-99172400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr10:99168800-99172600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr10:99168800-99178000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr10:99169000-99172400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr10:99169000-99172400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr10:99169000-99172600	Weak transcription	Placenta	Placenta
49	chr10:99169400-99175200	Enhancers	Primary neutrophils fromperipheralblood	blood
50	chr10:99169600-99173400	Weak transcription	Primary B cells from cord blood	blood

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