Variant report

Variant	rs10888419
Chromosome Location	chr1:151484219-151484220
allele	A/C
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151428938..151433041-chr1:151480813..151490135,53	MCF-7	breast:
2	chr1:151481429..151491154-chr1:151502501..151517487,49	MCF-7	breast:
3	chr1:151481542..151488437-chr1:151515636..151525415,14	MCF-7	breast:
4	chr1:151482538..151486660-chr1:151496961..151502245,5	MCF-7	breast:
5	chr1:151483025..151485659-chr1:152019731..152022240,2	MCF-7	breast:
6	chr1:151410006..151411683-chr1:151482922..151485531,2	MCF-7	breast:
7	chr1:151483091..151485437-chr1:151490674..151493564,2	K562	blood:
8	chr1:151477348..151494376-chr1:151504804..151515249,50	MCF-7	breast:
9	chr1:151414283..151420812-chr1:151481565..151487481,13	MCF-7	breast:
10	chr1:151481758..151484470-chr1:151811083..151813836,2	MCF-7	breast:
11	chr1:151483462..151487382-chr1:151518217..151524477,9	MCF-7	breast:
12	chr1:151414651..151422317-chr1:151482271..151486624,12	MCF-7	breast:
13	chr1:151042074..151044319-chr1:151484025..151486310,2	MCF-7	breast:
14	chr1:151170179..151172284-chr1:151482238..151485195,2	MCF-7	breast:
15	chr1:151427202..151436068-chr1:151477865..151490153,60	MCF-7	breast:
16	chr1:151483888..151486262-chr1:151734424..151737312,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143450	Chromatin interaction
ENSG00000143458	Chromatin interaction
ENSG00000207606	Chromatin interaction
ENSG00000143436	Chromatin interaction
ENSG00000225556	Chromatin interaction
ENSG00000232536	Chromatin interaction
ENSG00000163191	Chromatin interaction
ENSG00000238711	Chromatin interaction
ENSG00000197622	Chromatin interaction
ENSG00000143367	Chromatin interaction
ENSG00000143375	Chromatin interaction
ENSG00000143442	Chromatin interaction
ENSG00000143398	Chromatin interaction
ENSG00000252840	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1009289	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10127622	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10788807	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10788808	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10888418	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204827	1.00[JPT][hapmap]
rs11204828	1.00[JPT][hapmap]
rs11204834	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11204835	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11204837	0.94[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11204838	0.83[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11204839	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11583133	0.94[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11801161	0.84[JPT][hapmap]
rs12026585	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12032983	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12037100	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12118440	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12128578	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12730114	0.94[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1547832	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1573129	0.83[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap]
rs1573130	0.83[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2211435	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2298167	0.83[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2298168	0.83[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2337359	0.83[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2878950	0.84[JPT][hapmap]
rs4970955	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs61261719	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6675984	0.82[ASN][1000 genomes]
rs7548090	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7552458	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.88[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	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10888419	SPRR2B	cis	parietal	SCAN
rs10888419	TUFT1	cis	cerebellum	SCAN
rs10888419	SV2A	cis	parietal	SCAN
rs10888419	S100A2	cis	parietal	SCAN
rs10888419	OTUD7B	cis	cerebellum	SCAN
rs10888419	SCNM1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151482400-151485000	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr1:151482400-151486200	Active TSS	H9 Cell Line	embryonic stem cell
3	chr1:151482600-151484400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:151482600-151484400	Active TSS	Fetal Brain Female	brain
5	chr1:151482600-151485000	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr1:151482800-151484600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:151482800-151484800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr1:151482800-151485000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:151482800-151485000	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr1:151482800-151486000	Active TSS	Rectal Smooth Muscle	rectum
11	chr1:151483000-151484400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:151483000-151484400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:151483000-151484400	Active TSS	Primary T helper naive cells from peripheral blood	blood
14	chr1:151483000-151484400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr1:151483000-151484400	Active TSS	Brain Angular Gyrus	brain
16	chr1:151483000-151484400	Active TSS	Brain Hippocampus Middle	brain
17	chr1:151483000-151484400	Active TSS	Brain Substantia Nigra	brain
18	chr1:151483000-151484400	Active TSS	NHLF	lung
19	chr1:151483000-151484600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:151483000-151484800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:151483000-151485000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:151483200-151484400	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr1:151483200-151484400	Active TSS	A549	lung
24	chr1:151483200-151484600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:151483200-151484600	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr1:151483200-151484600	Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr1:151483200-151484600	Active TSS	Fetal Heart	heart
28	chr1:151483200-151484800	Active TSS	Psoas Muscle	Psoas
29	chr1:151483200-151484800	Flanking Active TSS	HMEC	breast
30	chr1:151483200-151484800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
31	chr1:151483200-151485000	Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr1:151483200-151485400	Active TSS	H1 Cell Line	embryonic stem cell
33	chr1:151483200-151485800	Active TSS	Small Intestine	intestine
34	chr1:151483200-151486200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:151483400-151484400	Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr1:151483400-151484400	Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr1:151483400-151484400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:151483400-151484400	Active TSS	HSMM	muscle
39	chr1:151483400-151484600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr1:151483400-151484600	Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr1:151483400-151484800	Active TSS	Fetal Intestine Large	intestine
42	chr1:151483400-151484800	Active TSS	Pancreas	Pancrea
43	chr1:151483400-151485000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:151483400-151485000	Active TSS	Lung	lung
45	chr1:151483400-151485400	Active TSS	Gastric	stomach
46	chr1:151483600-151484400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:151483600-151484400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
48	chr1:151483600-151484400	Active TSS	Fetal Intestine Small	intestine
49	chr1:151483600-151484400	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr1:151483800-151484600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle

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