Variant report

Variant	rs6698109
Chromosome Location	chr1:185171869-185171870
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	chr1:185169820..185172911-chr1:185283912..185286958,3	K562	blood:
2	chr1:185171608..185173207-chr1:185196628..185199212,2	K562	blood:

Variant related genes	Relation type
ENSG00000116679	Chromatin interaction
ENSG00000213051	Chromatin interaction
ENSG00000273004	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10218496	0.83[EUR][1000 genomes]
rs10453829	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs10489579	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs10489580	1.00[CEU][hapmap];0.89[GIH][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs10798000	1.00[CEU][hapmap];0.89[GIH][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs10911693	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs12024023	1.00[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12028408	0.98[EUR][1000 genomes]
rs12045671	0.98[EUR][1000 genomes]
rs12096987	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs12118722	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12119471	0.80[EUR][1000 genomes]
rs12120377	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12127840	0.80[EUR][1000 genomes]
rs12135172	0.92[CEU][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs12141722	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12404187	1.00[CEU][hapmap];0.89[GIH][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs1336752	0.92[CEU][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1415072	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs1591585	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1969750	0.99[EUR][1000 genomes]
rs2025227	0.98[EUR][1000 genomes]
rs2050566	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs2146328	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs2383269	0.92[CEU][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs3766717	0.95[EUR][1000 genomes]
rs57188163	0.98[EUR][1000 genomes]
rs57731138	0.94[EUR][1000 genomes]
rs6424972	1.00[CEU][hapmap];0.89[GIH][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes]
rs6424974	0.84[EUR][1000 genomes]
rs6660169	1.00[CEU][hapmap];0.89[GIH][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs6666742	0.92[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs6670117	0.98[EUR][1000 genomes]
rs6673303	1.00[CEU][hapmap];0.89[GIH][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs6698122	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs7512290	1.00[CEU][hapmap];0.89[GIH][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs7522617	0.99[EUR][1000 genomes]
rs7533198	1.00[CEU][hapmap];0.89[GIH][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs7535064	0.82[EUR][1000 genomes]
rs7539658	0.92[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs7543962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7550586	0.92[CEU][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7552662	0.98[EUR][1000 genomes]
rs7556183	0.99[EUR][1000 genomes]
rs951428	0.92[CEU][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
4	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
rs6698109	RNASEL	cis	parietal	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185127400-185192000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:185127600-185184600	Weak transcription	Psoas Muscle	Psoas
3	chr1:185127600-185218200	Weak transcription	Right Ventricle	heart
4	chr1:185128400-185193800	Weak transcription	Brain Angular Gyrus	brain
5	chr1:185128400-185201800	Weak transcription	Gastric	stomach
6	chr1:185131600-185173000	Weak transcription	Brain Substantia Nigra	brain
7	chr1:185134600-185193200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr1:185137200-185177200	Weak transcription	Primary B cells from cord blood	blood
9	chr1:185137200-185191400	Weak transcription	Brain Anterior Caudate	brain
10	chr1:185137400-185177400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:185137400-185191200	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:185137400-185191400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:185138000-185182200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:185138000-185186200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:185138000-185204000	Weak transcription	Colon Smooth Muscle	Colon
16	chr1:185139600-185177400	Weak transcription	Fetal Kidney	kidney
17	chr1:185139800-185191400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:185140000-185190800	Weak transcription	Primary B cells from peripheral blood	blood
19	chr1:185140000-185191600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr1:185144800-185181200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:185145000-185182400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:185145200-185191400	Weak transcription	Stomach Smooth Muscle	stomach
23	chr1:185148400-185193400	Weak transcription	Fetal Thymus	thymus
24	chr1:185151000-185193200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr1:185152200-185200800	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr1:185153200-185191600	Weak transcription	Aorta	Aorta
27	chr1:185154400-185191600	Weak transcription	Ovary	ovary
28	chr1:185158600-185176400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr1:185159600-185177600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:185160000-185192600	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr1:185160600-185191600	Weak transcription	Brain Germinal Matrix	brain
32	chr1:185160800-185192000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr1:185161800-185191400	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr1:185162000-185190800	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr1:185162200-185173800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr1:185163600-185190600	Weak transcription	Placenta	Placenta
37	chr1:185167400-185174600	Weak transcription	Fetal Lung	lung
38	chr1:185167600-185174800	Weak transcription	Duodenum Mucosa	Duodenum
39	chr1:185167600-185177400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:185167600-185177600	Weak transcription	Liver	Liver
41	chr1:185167800-185182200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:185168000-185201800	Weak transcription	Primary T cells from cord blood	blood
43	chr1:185168200-185191400	Weak transcription	Fetal Muscle Trunk	muscle
44	chr1:185168400-185192200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:185169400-185177800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr1:185170000-185172200	Strong transcription	Adipose Nuclei	Adipose
47	chr1:185170000-185172400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr1:185170000-185179600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:185170400-185174400	Weak transcription	Fetal Stomach	stomach
50	chr1:185170400-185192000	Weak transcription	Fetal Intestine Large	intestine

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