Variant report

Variant	rs2303307
Chromosome Location	chr1:85039955-85039956
allele	A/G
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:14)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:84966614..84978118-chr1:85034515..85041986,38	K562	blood:
2	chr1:85038587..85040484-chr1:85154316..85157145,3	K562	blood:
3	chr1:84966967..84974535-chr1:85036439..85041823,24	K562	blood:
4	chr1:84943703..84948095-chr1:85037647..85043843,8	K562	blood:
5	chr1:85039171..85040042-chr3:152879140..152880139,2	Hela-S3	cervix:
6	chr1:85039736..85040735-chr9:128003564..128004223,2	Hela-S3	cervix:
7	chr1:85039593..85040467-chr7:112090793..112091301,2	NB4	blood:
8	chr1:84943714..84946459-chr1:85038706..85040687,2	K562	blood:
9	chr1:85039820..85040684-chr12:31476818..31477702,2	HCT-116	colon:
10	chr1:85038984..85041113-chr1:85155645..85157338,2	K562	blood:
11	chr1:84981895..84983594-chr1:85038759..85040423,2	K562	blood:
12	chr1:85039843..85040683-chr12:53894216..53894768,2	HCT-116	colon:
13	chr1:85039501..85040254-chr1:151512684..151513325,2	Hela-S3	cervix:
14	chr1:85039718..85040687-chr2:99224792..99225429,2	Hela-S3	cervix:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTBS-1	chr1:85039922-85040163	NONHSAT004214

No data

Variant related genes	Relation type
ENSG00000139146	Chromatin interaction
ENSG00000117155	Chromatin interaction
ENSG00000239705	Chromatin interaction
ENSG00000139546	Chromatin interaction
ENSG00000006652	Chromatin interaction
ENSG00000174021	Chromatin interaction
ENSG00000122432	Chromatin interaction
ENSG00000183513	Chromatin interaction
ENSG00000117133	Chromatin interaction
ENSG00000177340	Chromatin interaction
ENSG00000181467	Chromatin interaction
ENSG00000232536	Chromatin interaction
ENSG00000044574	Chromatin interaction
ENSG00000244268	Chromatin interaction
ENSG00000143367	Chromatin interaction
ENSG00000270175	Chromatin interaction
ENSG00000115446	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs12131448	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs12137275	0.81[EUR][1000 genomes]
rs12141472	0.93[CEU][hapmap]
rs12403545	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs1246253	0.81[CHB][hapmap]
rs1246254	0.81[CHB][hapmap];0.94[CHD][hapmap]
rs1400777	0.94[CHD][hapmap]
rs1417295	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2203455	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2292191	0.81[CHB][hapmap]
rs2303306	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2911588	0.97[ASN][1000 genomes]
rs2911589	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2911590	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2911591	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2911592	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2911594	0.80[EUR][1000 genomes]
rs2911597	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2911598	0.87[CEU][hapmap];0.85[CHB][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2911599	0.94[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2911607	0.86[EUR][1000 genomes]
rs2911609	0.84[EUR][1000 genomes]
rs2943671	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2943675	0.94[ASN][1000 genomes]
rs2943676	0.94[ASN][1000 genomes]
rs2943677	0.94[ASN][1000 genomes]
rs2943678	0.98[ASN][1000 genomes]
rs2945143	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2945145	0.88[CEU][hapmap];0.88[MEX][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2945146	0.82[ASN][1000 genomes]
rs2945147	0.88[CEU][hapmap];0.82[MEX][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2945148	0.82[ASN][1000 genomes]
rs2945150	0.88[ASN][1000 genomes]
rs2945152	0.87[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs2945153	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2945155	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2945158	0.96[ASN][1000 genomes]
rs2945160	0.94[ASN][1000 genomes]
rs2994934	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2994935	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2994937	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2994938	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2994940	0.82[ASN][1000 genomes]
rs2994946	0.94[ASN][1000 genomes]
rs2994948	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs2994953	0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2994954	0.81[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.85[ASN][1000 genomes]
rs2994955	0.84[ASN][1000 genomes]
rs3021402	0.81[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.83[ASN][1000 genomes]
rs41299545	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4356070	0.82[EUR][1000 genomes]
rs4906997	0.83[ASN][1000 genomes]
rs6576713	0.81[CHB][hapmap];0.94[CHD][hapmap]
rs6692765	0.86[CHB][hapmap];0.85[JPT][hapmap]

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	nsv1000325	chr1:85032605-85100748	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2303307	SPATA1	cis	parietal	SCAN
rs2303307	BCL10	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85037400-85041200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:85037800-85041200	Active TSS	GM12878-XiMat	blood
3	chr1:85038200-85040000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:85038200-85041000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:85038400-85040000	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr1:85038400-85040600	Active TSS	Colonic Mucosa	Colon
7	chr1:85038400-85040800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:85038600-85040000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:85038600-85040600	Active TSS	H9 Cell Line	embryonic stem cell
10	chr1:85038600-85040600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:85038600-85040600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:85038600-85040600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:85038600-85040600	Flanking Active TSS	HUVEC	blood vessel
14	chr1:85038600-85040600	Active TSS	K562	blood
15	chr1:85038600-85040800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:85038600-85040800	Active TSS	Psoas Muscle	Psoas
17	chr1:85038600-85040800	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr1:85038600-85041000	Active TSS	Fetal Kidney	kidney
19	chr1:85038800-85040000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:85038800-85040000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:85038800-85040000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
22	chr1:85038800-85040000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:85038800-85040000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr1:85038800-85040400	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr1:85038800-85040400	Active TSS	Fetal Muscle Leg	muscle
26	chr1:85038800-85041000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:85039000-85040400	Active TSS	Brain Angular Gyrus	brain
28	chr1:85039000-85040600	Active TSS	H1 Cell Line	embryonic stem cell
29	chr1:85039000-85040600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr1:85039000-85040600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:85039000-85040600	Active TSS	Fetal Brain Male	brain
32	chr1:85039000-85040600	Active TSS	Right Ventricle	heart
33	chr1:85039000-85040600	Active TSS	Sigmoid Colon	Sigmoid Colon
34	chr1:85039000-85040600	Active TSS	NHLF	lung
35	chr1:85039000-85040800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:85039000-85040800	Active TSS	HSMMtube	muscle
37	chr1:85039200-85040000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr1:85039200-85040400	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr1:85039200-85040400	Active TSS	Liver	Liver
40	chr1:85039200-85040400	Active TSS	Small Intestine	intestine
41	chr1:85039200-85040400	Active TSS	NHEK	skin
42	chr1:85039200-85040600	Active TSS	Brain Substantia Nigra	brain
43	chr1:85039200-85040600	Active TSS	Fetal Intestine Small	intestine
44	chr1:85039200-85040600	Active TSS	Left Ventricle	heart
45	chr1:85039200-85040600	Active TSS	Lung	lung
46	chr1:85039200-85040600	Active TSS	Ovary	ovary
47	chr1:85039200-85040600	Active TSS	HSMM	muscle
48	chr1:85039200-85040800	Active TSS	Rectal Mucosa Donor 31	rectum
49	chr1:85039200-85041000	Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr1:85039200-85041200	Active TSS	Breast Myoepithelial Primary Cells	Breast

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