Variant report

Variant	rs1556796
Chromosome Location	chr1:97979675-97979676
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10493893	0.87[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10875094	0.87[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10875095	0.85[AFR][1000 genomes]
rs11165882	0.85[LWK][hapmap];0.89[YRI][hapmap]
rs11165886	0.87[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs11165887	0.87[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs11165889	0.87[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs12029826	0.88[ASN][1000 genomes]
rs12032158	0.87[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs12034649	0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs1337752	0.97[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs1556795	0.87[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.91[ASN][1000 genomes]
rs1556797	0.91[ASN][1000 genomes]
rs17116810	0.87[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.92[ASN][1000 genomes]
rs2027250	0.88[AFR][1000 genomes]
rs2105129	0.92[YRI][hapmap];0.87[AFR][1000 genomes]
rs2786512	0.97[LWK][hapmap];0.88[MKK][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs2786770	0.82[AFR][1000 genomes]
rs2786781	0.82[AFR][1000 genomes]
rs2786782	0.81[MKK][hapmap];0.86[YRI][hapmap]
rs2786784	0.89[AFR][1000 genomes]
rs2811172	0.81[AFR][1000 genomes]
rs2811173	0.83[LWK][hapmap];0.81[MKK][hapmap]
rs2811174	0.97[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs2811175	0.85[AFR][1000 genomes]
rs2811176	0.88[AFR][1000 genomes]
rs2811177	0.97[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs2811178	0.80[AFR][1000 genomes]
rs2811182	0.97[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs2811184	0.86[YRI][hapmap]
rs2811186	0.80[AFR][1000 genomes]
rs4364915	0.86[YRI][hapmap]
rs4427441	0.82[AFR][1000 genomes]
rs4949955	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6671771	0.82[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs7516492	0.92[ASN][1000 genomes]
rs7519652	0.87[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7545340	0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491816	chr1:97266403-98223619	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv530048	chr1:97457175-98031501	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1007950	chr1:97466488-98021146	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv533039	chr1:97665736-98343102	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv530049	chr1:97883261-98384614	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv830703	chr1:97907708-98101144	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv519191	chr1:97945292-98000861	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv947294	chr1:97978512-97983491	Weak transcription Enhancers Strong transcription	n/a	n/a	inside rSNPs	diseases
9	esv3357734	chr1:97979399-97979952	Strong transcription Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1556796	PCIF1	trans	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:97872600-98014600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:97928600-98018200	Weak transcription	Ovary	ovary
3	chr1:97955800-97990000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:97956400-98009400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:97963000-98009400	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr1:97964600-98010400	Weak transcription	Dnd41	blood
7	chr1:97965000-97985200	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr1:97966400-97988400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr1:97967200-97982600	Weak transcription	Pancreas	Pancrea
10	chr1:97967200-97982600	Weak transcription	HSMM	muscle
11	chr1:97972000-97985600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr1:97972200-97985200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:97972400-97983400	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr1:97972400-97988600	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr1:97973800-97996200	Weak transcription	Osteobl	bone
16	chr1:97974800-97981400	Weak transcription	Lung	lung
17	chr1:97976000-97983400	Weak transcription	Fetal Heart	heart
18	chr1:97976400-97980400	Weak transcription	Fetal Lung	lung
19	chr1:97976400-97982400	Weak transcription	Brain Substantia Nigra	brain
20	chr1:97976400-97983000	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr1:97976600-97999000	Weak transcription	Liver	Liver
22	chr1:97976600-98014600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:97976600-98054200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:97976800-97981400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:97976800-97981800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr1:97976800-97985200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:97976800-97988200	Weak transcription	Primary T cells from cord blood	blood
28	chr1:97976800-98009400	Weak transcription	Primary B cells from cord blood	blood
29	chr1:97976800-98051400	Weak transcription	Left Ventricle	heart
30	chr1:97977400-97986800	Weak transcription	Primary hematopoietic stem cells	blood
31	chr1:97978600-97983800	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr1:97979200-97980000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:97979600-97980800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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