Variant report

Variant	rs3737787
Chromosome Location	chr1:161009523-161009524
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:161009434-161009841	K562	blood:	n/a	n/a
2	ELF1	chr1:161009217-161009701	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:161009108-161009819	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:161009501-161009527	MCF-7	breast:	n/a	n/a
5	POLR2A	chr1:161009099-161009698	GM12892	blood:	n/a	n/a
6	POLR2A	chr1:161009077-161009726	K562	blood:	n/a	n/a
7	POLR2A	chr1:161009185-161009540	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:161007165..161010190-chr1:161058502..161060475,3	MCF-7	breast:
2	chr1:161007047..161009717-chr1:161100084..161102311,2	K562	blood:
3	chr1:160989087..160991942-chr1:161007144..161014242,6	K562	blood:
4	chr1:161007801..161009697-chr1:161067796..161070375,2	K562	blood:
5	chr1:161006354..161009878-chr1:161042497..161045575,4	MCF-7	breast:
6	chr1:160988819..160994033-chr1:161005548..161011188,8	MCF-7	breast:
7	chr1:161007064..161010778-chr1:161101040..161104167,3	MCF-7	breast:
8	chr1:160989495..160995605-chr1:161004888..161010340,15	MCF-7	breast:
9	chr1:161006846..161009787-chr1:161123441..161125743,2	MCF-7	breast:
10	chr1:160988071..160992174-chr1:161007125..161014242,7	K562	blood:
11	chr1:161005808..161012985-chr1:161064732..161070101,9	MCF-7	breast:

No data

Variant related genes	Relation type
TSTD1	TF binding region
ENSG00000270149	TF binding region
ENSG00000162755	Chromatin interaction
ENSG00000158769	Chromatin interaction
ENSG00000158796	Chromatin interaction
ENSG00000143217	Chromatin interaction
ENSG00000143222	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1044478	0.91[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes]
rs1062826	0.87[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes]
rs1062827	0.87[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes]
rs11265540	0.82[AMR][1000 genomes]
rs11265542	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11799478	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11799521	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11801591	0.85[CHB][hapmap];1.00[YRI][hapmap]
rs11802727	1.00[YRI][hapmap]
rs11807930	0.87[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes]
rs12401336	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12403334	0.88[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap]
rs12408778	0.80[AMR][1000 genomes]
rs12565932	0.87[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes]
rs1556519	1.00[YRI][hapmap]
rs17384360	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs17388108	0.87[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1806774	0.85[AMR][1000 genomes]
rs2073655	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2073656	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2073658	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2243427	0.83[AMR][1000 genomes]
rs2247459	0.87[CEU][hapmap];0.85[CHB][hapmap];0.83[AMR][1000 genomes]
rs2247596	0.87[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes]
rs2247671	0.87[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes]
rs2247790	0.87[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes]
rs2251597	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2251728	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2297219	0.87[AMR][1000 genomes]
rs2297220	0.87[CEU][hapmap];0.92[CHB][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs2297221	0.87[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes]
rs2297222	0.86[CEU][hapmap];0.87[AMR][1000 genomes]
rs2481080	0.87[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes]
rs2481081	0.87[CEU][hapmap];0.88[CHB][hapmap];0.80[JPT][hapmap];0.83[AMR][1000 genomes]
rs2481083	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2481084	0.87[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2481085	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2483145	0.83[AMR][1000 genomes]
rs2774274	0.83[AMR][1000 genomes]
rs2988726	0.83[AMR][1000 genomes]
rs3119321	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3737785	0.83[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes]
rs41267947	0.87[AMR][1000 genomes]
rs41267949	0.87[AMR][1000 genomes]
rs41267951	0.87[AMR][1000 genomes]
rs41269993	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4339888	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55728374	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61803664	0.87[AMR][1000 genomes]
rs61803671	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61803672	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72712854	0.85[AMR][1000 genomes]
rs812741	0.83[AMR][1000 genomes]
rs836	0.87[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes]
rs869985	0.87[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.87[AMR][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	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv947201	chr1:161006051-161013276	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv548059	chr1:161007326-161010791	Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv3221	chr1:161008175-161052979	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv872492	chr1:161009523-161013152	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3737787	FCRL1	cis	cerebellum	SCAN
rs3737787	OR6K6	cis	cerebellum	SCAN
rs3737787	OR10J5	cis	cerebellum	SCAN
rs3737787	F11R	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161007000-161013400	Strong transcription	Cortex derived primary cultured neurospheres	brain
2	chr1:161007400-161013400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr1:161007400-161013400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:161007400-161013400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:161007400-161013400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:161007600-161013400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:161008000-161013200	Strong transcription	A549	lung
8	chr1:161008000-161013400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:161008200-161013000	Strong transcription	NHLF	lung
10	chr1:161008600-161009600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:161008600-161009800	Weak transcription	Fetal Heart	heart
12	chr1:161008600-161011400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:161008800-161012600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:161008800-161013000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:161008800-161013400	Strong transcription	Brain Cingulate Gyrus	brain
16	chr1:161008800-161014000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr1:161009000-161009600	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:161009000-161009600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
19	chr1:161009000-161009600	Genic enhancers	Placenta	Placenta
20	chr1:161009000-161009600	Genic enhancers	HSMM	muscle
21	chr1:161009000-161009600	Genic enhancers	Monocytes-CD14+_RO01746	blood
22	chr1:161009000-161009800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr1:161009000-161009800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:161009000-161009800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
25	chr1:161009000-161010000	Genic enhancers	Colonic Mucosa	Colon
26	chr1:161009000-161010000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr1:161009000-161010000	Genic enhancers	Fetal Muscle Leg	muscle
28	chr1:161009000-161010000	Genic enhancers	Fetal Thymus	thymus
29	chr1:161009000-161010000	Weak transcription	Ovary	ovary
30	chr1:161009000-161010400	Genic enhancers	Spleen	Spleen
31	chr1:161009000-161011800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr1:161009000-161012400	Weak transcription	Psoas Muscle	Psoas
33	chr1:161009000-161012600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:161009000-161012800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:161009000-161012800	Strong transcription	Adipose Nuclei	Adipose
36	chr1:161009000-161013200	Strong transcription	Osteobl	bone
37	chr1:161009000-161013400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:161009000-161013400	Strong transcription	Fetal Stomach	stomach
39	chr1:161009000-161014000	Genic enhancers	Primary B cells from peripheral blood	blood
40	chr1:161009200-161009600	Genic enhancers	H1 Cell Line	embryonic stem cell
41	chr1:161009200-161009600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr1:161009200-161009600	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
43	chr1:161009200-161009600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr1:161009200-161009600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:161009200-161009600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:161009200-161009600	Transcr. at gene 5' and 3'	Liver	Liver
47	chr1:161009200-161009600	Genic enhancers	Brain Germinal Matrix	brain
48	chr1:161009200-161009600	Genic enhancers	Fetal Intestine Large	intestine
49	chr1:161009200-161009600	Genic enhancers	Fetal Intestine Small	intestine
50	chr1:161009200-161009600	Genic enhancers	Fetal Muscle Trunk	muscle

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