Variant report

Variant	rs860295
Chromosome Location	chr1:155767708-155767709
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:155698585..155701344-chr1:155765274..155767942,2	K562	blood:

Variant related genes	Relation type
ENSG00000132676	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10796954	0.80[ASN][1000 genomes]
rs10908479	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs10908481	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.83[ASN][1000 genomes]
rs10908482	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11264409	0.83[ASN][1000 genomes]
rs11264410	0.93[ASN][1000 genomes]
rs11264413	0.86[ASN][1000 genomes]
rs12024187	0.81[ASN][1000 genomes]
rs12024257	0.83[ASN][1000 genomes]
rs12035524	0.85[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap]
rs12040894	0.97[ASN][1000 genomes]
rs12047756	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs12407800	0.91[ASN][1000 genomes]
rs12563627	0.80[JPT][hapmap];0.83[MEX][hapmap]
rs12744132	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs1749405	0.80[JPT][hapmap];0.82[MEX][hapmap]
rs1973768	0.82[ASN][1000 genomes]
rs2048431	0.85[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap]
rs2175391	0.85[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap]
rs2297775	0.89[ASN][1000 genomes]
rs28582361	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2948071	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2948072	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2985707	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2993207	0.80[JPT][hapmap];0.83[MEX][hapmap]
rs348196	0.85[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap]
rs3738590	0.84[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap]
rs3820594	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs4278368	0.83[ASN][1000 genomes]
rs4661151	0.83[MEX][hapmap]
rs4661175	0.87[MEX][hapmap]
rs475550	0.97[CHD][hapmap];0.82[JPT][hapmap]
rs488079	0.80[JPT][hapmap];0.82[MEX][hapmap]
rs490608	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs625658	0.80[JPT][hapmap];0.83[MEX][hapmap]
rs6427286	0.95[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6427287	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs644853	0.93[YRI][hapmap]
rs6657670	0.86[ASN][1000 genomes]
rs6662953	0.95[ASN][1000 genomes]
rs6665227	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs670876	0.85[CHB][hapmap]
rs678157	0.82[JPT][hapmap]
rs708611	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs729022	0.85[CEU][hapmap];0.80[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap]
rs7541060	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7550402	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs821551	0.92[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs822025	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs822478	0.90[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs822490	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs822505	0.84[CEU][hapmap];0.80[JPT][hapmap]
rs822508	0.85[CEU][hapmap];0.80[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap]
rs822527	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9426933	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv428246	chr1:155558197-155785831	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3423892	chr1:155664084-155901487	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv872469	chr1:155743310-155810293	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1003170	chr1:155762204-155836564	Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs860295	SPRR3	cis	parietal	SCAN
rs860295	RIT1	cis	cerebellum	SCAN
rs860295	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs860295	BCAN	cis	cerebellum	SCAN
rs860295	YY1AP1	cis	cerebellum	SCAN
rs860295	PRUNE	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155715400-155789200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:155716000-155793400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:155716600-155781800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:155717400-155795800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:155720200-155798200	Strong transcription	Fetal Thymus	thymus
6	chr1:155720200-155803600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:155720400-155796800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr1:155732200-155789200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:155737200-155772200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:155743200-155773400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr1:155746400-155774000	Weak transcription	Pancreas	Pancrea
12	chr1:155746400-155791400	Weak transcription	Stomach Mucosa	stomach
13	chr1:155747600-155776200	Weak transcription	Right Ventricle	heart
14	chr1:155747600-155787200	Weak transcription	Esophagus	oesophagus
15	chr1:155747800-155785600	Weak transcription	Fetal Brain Male	brain
16	chr1:155747800-155791200	Weak transcription	Fetal Heart	heart
17	chr1:155748000-155789400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:155748800-155771600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr1:155751800-155777600	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr1:155752000-155771000	Strong transcription	Fetal Muscle Leg	muscle
21	chr1:155754800-155770600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr1:155755000-155772600	Weak transcription	Gastric	stomach
23	chr1:155755200-155768600	Weak transcription	HSMMtube	muscle
24	chr1:155755200-155771600	Weak transcription	Small Intestine	intestine
25	chr1:155755200-155774000	Weak transcription	Colonic Mucosa	Colon
26	chr1:155755400-155768400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:155755600-155777400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr1:155758000-155777200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:155758200-155777200	Strong transcription	Fetal Intestine Large	intestine
30	chr1:155758800-155778400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:155759000-155777200	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr1:155759200-155777400	Strong transcription	Placenta	Placenta
33	chr1:155760200-155770800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr1:155760200-155777200	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr1:155760400-155779000	Strong transcription	Thymus	Thymus
36	chr1:155760800-155777200	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr1:155761600-155776800	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr1:155761600-155778400	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr1:155761800-155777000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr1:155761800-155777200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr1:155762000-155777200	Strong transcription	Liver	Liver
42	chr1:155762200-155769800	Strong transcription	Duodenum Mucosa	Duodenum
43	chr1:155762200-155775000	Strong transcription	Primary B cells from peripheral blood	blood
44	chr1:155762200-155798000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:155762600-155770600	Strong transcription	Left Ventricle	heart
46	chr1:155762600-155779200	Strong transcription	Fetal Stomach	stomach
47	chr1:155762600-155785000	Strong transcription	Fetal Intestine Small	intestine
48	chr1:155762800-155779200	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr1:155763000-155773600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr1:155763000-155779000	Strong transcription	HUES6 Cell Line	embryonic stem cell

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