Variant report

Variant	rs2061799
Chromosome Location	chr9:97795004-97795005
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:97786821..97789606-chr9:97794967..97796572,3	K562	blood:
2	chr9:97794089..97795756-chr9:97801437..97804399,2	K562	blood:
3	chr9:97793038..97795418-chr9:97797884..97800566,2	K562	blood:
4	chr9:97792211..97795140-chr9:97806961..97811123,4	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HIATL1-7	chr9:97794314-97795781	ENSG00000251631
2	lnc-FANCC-3	chr9:97794312-97795781	NONHSAT133343

No data

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1020962	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10217441	1.00[CEU][hapmap]
rs1038092	1.00[CEU][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10732407	1.00[CEU][hapmap]
rs10761362	1.00[CEU][hapmap]
rs10761371	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs10993471	0.86[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs12554043	0.81[GIH][hapmap]
rs12683030	0.86[JPT][hapmap]
rs1530331	0.81[GIH][hapmap]
rs1542107	0.81[GIH][hapmap]
rs1542108	1.00[CEU][hapmap]
rs1564235	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1571896	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1571897	0.82[CHD][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1871220	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1888944	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1888945	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1888946	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2026399	0.81[GIH][hapmap]
rs2061798	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2061801	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2095069	0.81[GIH][hapmap]
rs2306207	0.86[MEX][hapmap];1.00[TSI][hapmap]
rs2406898	0.81[GIH][hapmap]
rs3739748	1.00[CEU][hapmap];0.86[MEX][hapmap];0.96[EUR][1000 genomes]
rs3802449	0.86[JPT][hapmap]
rs3886568	0.81[GIH][hapmap]
rs400727	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs4332191	1.00[CEU][hapmap]
rs4647549	0.86[JPT][hapmap]
rs4743972	1.00[CEU][hapmap]
rs4743975	1.00[CEU][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4743976	0.87[GIH][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4743977	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4743978	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4744421	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6479578	1.00[CEU][hapmap]
rs6479589	0.82[MEX][hapmap];0.82[AMR][1000 genomes]
rs6479596	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479597	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7019602	1.00[CEU][hapmap]
rs7022739	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022963	1.00[CEU][hapmap]
rs7023719	1.00[CEU][hapmap]
rs7025100	1.00[CEU][hapmap]
rs7029570	0.81[GIH][hapmap]
rs7035166	0.81[GIH][hapmap]
rs7039768	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7042271	0.88[MEX][hapmap]
rs7867856	1.00[CEU][hapmap]
rs7869736	0.81[GIH][hapmap]
rs894426	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1038106	chr9:97793038-97881416	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2061799	KIAA1199	trans	brain	seeQTL
rs2061799	GMDS	trans	brain	seeQTL
rs2061799	SLPI	trans	brain	seeQTL
rs2061799	OLFML2A	trans	brain	seeQTL
rs2061799	KLF2	trans	brain	seeQTL
rs2061799	ANXA2	trans	brain	seeQTL
rs2061799	BMP6	trans	brain	seeQTL
rs2061799	GJB2	trans	brain	seeQTL
rs2061799	OMD	trans	brain	seeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97770800-97810000	Weak transcription	Primary T cells from cord blood	blood
2	chr9:97787800-97795800	Genic enhancers	Osteobl	bone
3	chr9:97788400-97795800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr9:97788800-97795800	Enhancers	Psoas Muscle	Psoas
5	chr9:97789000-97806200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr9:97790000-97795800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr9:97790000-97796800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr9:97790200-97795600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr9:97790200-97795800	Enhancers	Right Atrium	heart
10	chr9:97790200-97796000	Enhancers	Brain Angular Gyrus	brain
11	chr9:97790200-97796400	Genic enhancers	HSMM	muscle
12	chr9:97790600-97795800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr9:97790800-97795600	Genic enhancers	Fetal Intestine Small	intestine
14	chr9:97791200-97795600	Genic enhancers	Liver	Liver
15	chr9:97791200-97795800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr9:97791400-97795800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr9:97791600-97799600	Weak transcription	Hela-S3	cervix
18	chr9:97791600-97800000	Weak transcription	Placenta	Placenta
19	chr9:97791800-97795400	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr9:97792600-97795800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr9:97792800-97795600	Genic enhancers	Fetal Stomach	stomach
22	chr9:97792800-97795600	Enhancers	Right Ventricle	heart
23	chr9:97792800-97795800	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr9:97792800-97795800	Enhancers	Stomach Mucosa	stomach
25	chr9:97793000-97795800	Enhancers	Brain Cingulate Gyrus	brain
26	chr9:97793000-97795800	Enhancers	Pancreas	Pancrea
27	chr9:97793000-97796000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr9:97793000-97797200	Enhancers	Brain Substantia Nigra	brain
29	chr9:97793000-97800000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr9:97793200-97795400	Genic enhancers	Fetal Muscle Leg	muscle
31	chr9:97793200-97795800	Genic enhancers	HSMMtube	muscle
32	chr9:97793200-97796000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr9:97793200-97802200	Weak transcription	Fetal Kidney	kidney
34	chr9:97793400-97810400	Weak transcription	HUVEC	blood vessel
35	chr9:97793600-97795200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr9:97793600-97795600	Enhancers	Primary hematopoietic stem cells	blood
37	chr9:97793600-97795600	Enhancers	Fetal Intestine Large	intestine
38	chr9:97793600-97798200	Weak transcription	NHDF-Ad	bronchial
39	chr9:97793800-97795400	Enhancers	NHEK	skin
40	chr9:97793800-97795600	Enhancers	Duodenum Mucosa	Duodenum
41	chr9:97793800-97795600	Enhancers	Lung	lung
42	chr9:97793800-97795600	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr9:97793800-97795800	Enhancers	Brain Anterior Caudate	brain
44	chr9:97793800-97795800	Enhancers	Esophagus	oesophagus
45	chr9:97793800-97795800	Enhancers	Small Intestine	intestine
46	chr9:97793800-97800000	Weak transcription	Adipose Nuclei	Adipose
47	chr9:97794000-97795600	Enhancers	Spleen	Spleen
48	chr9:97794000-97796800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr9:97794000-97799800	Weak transcription	Fetal Lung	lung
50	chr9:97794200-97795200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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