Variant report

Variant	rs10489579
Chromosome Location	chr1:185143721-185143722
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr1:185143534-185143749	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:185140925..185143798-chr1:185185580..185188162,2	K562	blood:
2	chr1:185141715..185144712-chr1:185145189..185148552,4	K562	blood:

Variant related genes	Relation type
ENSG00000231084	TF binding region

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1008502	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs10218496	0.83[EUR][1000 genomes]
rs10453829	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10489580	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10489581	0.89[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap]
rs10798000	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10911674	0.89[CHB][hapmap];0.80[CHD][hapmap];0.81[JPT][hapmap]
rs10911693	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs12022419	0.89[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap]
rs12024023	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs12028408	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12035073	0.89[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap]
rs12037692	0.89[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap]
rs12038919	0.89[CHB][hapmap];0.80[CHD][hapmap];0.81[JPT][hapmap]
rs12043427	0.89[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs12043495	0.89[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap]
rs12043617	0.89[CHB][hapmap];0.80[CHD][hapmap]
rs12045671	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12046095	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs12096987	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12118722	0.83[EUR][1000 genomes]
rs12119471	0.80[EUR][1000 genomes]
rs12120377	0.81[EUR][1000 genomes]
rs12127840	0.80[EUR][1000 genomes]
rs12135172	0.92[CEU][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs12141722	0.97[EUR][1000 genomes]
rs12404187	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12408279	0.89[CHB][hapmap];0.80[CHD][hapmap]
rs12409926	0.89[CHB][hapmap];0.80[CHD][hapmap];0.81[JPT][hapmap]
rs1336752	0.92[CEU][hapmap];0.90[TSI][hapmap]
rs1407554	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs1415072	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1591585	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1969750	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2025227	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2050566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2146328	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2378958	0.89[CHB][hapmap];0.80[CHD][hapmap];0.81[JPT][hapmap]
rs2383269	0.85[ASW][hapmap];0.92[CEU][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3766717	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3766720	0.89[CHB][hapmap];0.80[CHD][hapmap]
rs3766723	0.89[CHB][hapmap];0.80[CHD][hapmap];0.81[JPT][hapmap]
rs57188163	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57731138	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6424972	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6424974	0.83[EUR][1000 genomes]
rs6660169	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6666742	0.92[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs6670117	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6673303	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6674490	0.84[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs6684586	0.85[CHD][hapmap];0.86[JPT][hapmap]
rs6698109	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs6698122	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7512290	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7522617	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7533198	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7535064	0.81[EUR][1000 genomes]
rs7539658	0.92[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs7543962	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs7550586	0.92[CEU][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs7552662	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7556183	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs951428	0.92[CEU][hapmap];0.90[TSI][hapmap];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	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv548396	chr1:185038104-185151378	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv521613	chr1:185071831-185171869	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv548398	chr1:185136458-186003094	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS 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 target site	69 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10489579	RNASEL	cis	parietal	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185127200-185147000	Weak transcription	Spleen	Spleen
2	chr1:185127200-185169800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:185127400-185144400	Weak transcription	Pancreas	Pancrea
4	chr1:185127400-185152200	Weak transcription	Aorta	Aorta
5	chr1:185127400-185153000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:185127400-185157400	Weak transcription	Small Intestine	intestine
7	chr1:185127400-185163400	Weak transcription	Esophagus	oesophagus
8	chr1:185127400-185192000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:185127600-185144400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:185127600-185144800	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr1:185127600-185145200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:185127600-185145400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:185127600-185147400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:185127600-185170000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:185127600-185184600	Weak transcription	Psoas Muscle	Psoas
16	chr1:185127600-185218200	Weak transcription	Right Ventricle	heart
17	chr1:185127800-185147000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:185128000-185166400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr1:185128200-185147200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr1:185128200-185153800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:185128200-185161200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:185128400-185145400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr1:185128400-185155200	Weak transcription	NHDF-Ad	bronchial
24	chr1:185128400-185193800	Weak transcription	Brain Angular Gyrus	brain
25	chr1:185128400-185201800	Weak transcription	Gastric	stomach
26	chr1:185128600-185168200	Weak transcription	Fetal Heart	heart
27	chr1:185128600-185171400	Weak transcription	Fetal Brain Male	brain
28	chr1:185131600-185173000	Weak transcription	Brain Substantia Nigra	brain
29	chr1:185132000-185155800	Weak transcription	HSMMtube	muscle
30	chr1:185134000-185170600	Weak transcription	Lung	lung
31	chr1:185134600-185193200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr1:185134800-185159800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:185135000-185162800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:185135800-185147200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:185136600-185167200	Weak transcription	Duodenum Mucosa	Duodenum
36	chr1:185136800-185171200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr1:185137200-185147800	Weak transcription	Primary T cells from cord blood	blood
38	chr1:185137200-185166800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:185137200-185177200	Weak transcription	Primary B cells from cord blood	blood
40	chr1:185137200-185191400	Weak transcription	Brain Anterior Caudate	brain
41	chr1:185137400-185144400	Weak transcription	Stomach Smooth Muscle	stomach
42	chr1:185137400-185147200	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr1:185137400-185152200	Weak transcription	Ovary	ovary
44	chr1:185137400-185154600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:185137400-185160000	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr1:185137400-185160200	Weak transcription	Brain Germinal Matrix	brain
47	chr1:185137400-185168000	Weak transcription	Fetal Intestine Large	intestine
48	chr1:185137400-185177400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:185137400-185191200	Weak transcription	Brain Hippocampus Middle	brain
50	chr1:185137400-185191400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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