Variant report

Variant	rs2061798
Chromosome Location	chr9:97794604-97794605
allele	A/C
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	chr9:97794089..97795756-chr9:97801437..97804399,2	K562	blood:
2	chr9:97793038..97795418-chr9:97797884..97800566,2	K562	blood:
3	chr9:97683038..97684583-chr9:97793134..97794968,2	MCF-7	breast:
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: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1020962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10217441	1.00[CEU][hapmap]
rs1038092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10732407	1.00[CEU][hapmap]
rs10761362	1.00[CEU][hapmap]
rs10761371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993471	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12553869	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12555128	1.00[JPT][hapmap]
rs12555829	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1542108	1.00[CEU][hapmap]
rs1564235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1571896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1571897	0.85[CHB][hapmap];0.88[AMR][1000 genomes]
rs16911834	1.00[JPT][hapmap]
rs16911856	1.00[JPT][hapmap]
rs1871220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888945	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888946	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061799	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[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2104888	1.00[JPT][hapmap]
rs2306207	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs242448	1.00[JPT][hapmap]
rs356685	1.00[JPT][hapmap]
rs356686	1.00[JPT][hapmap]
rs3739748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3780560	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4332191	1.00[CEU][hapmap]
rs4743972	1.00[CEU][hapmap]
rs4743975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743976	0.86[CHB][hapmap];0.88[AMR][1000 genomes]
rs4743977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743978	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743989	0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4744421	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744429	1.00[ASN][1000 genomes]
rs4744437	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4744440	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs475413	1.00[JPT][hapmap]
rs6479578	1.00[CEU][hapmap]
rs6479589	0.88[AMR][1000 genomes]
rs6479596	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6479597	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67134693	0.96[ASN][1000 genomes]
rs7019602	1.00[CEU][hapmap]
rs7022739	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7022963	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7023719	1.00[CEU][hapmap]
rs7025100	1.00[CEU][hapmap]
rs7039768	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7046900	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs72750335	0.96[ASN][1000 genomes]
rs72750346	0.96[ASN][1000 genomes]
rs72750351	0.96[ASN][1000 genomes]
rs72750359	0.96[ASN][1000 genomes]
rs72750367	1.00[ASN][1000 genomes]
rs72750373	1.00[ASN][1000 genomes]
rs73540087	1.00[ASN][1000 genomes]
rs7867856	1.00[CEU][hapmap]
rs894426	1.00[CEU][hapmap]
rs9299427	0.83[ASN][1000 genomes]

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

No data

Chromatin state (count:89 , 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	chr9:97788000-97794800	Genic enhancers	Muscle Satellite Cultured Cells	--
4	chr9:97788400-97795800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr9:97788800-97795000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr9:97788800-97795800	Enhancers	Psoas Muscle	Psoas
7	chr9:97789000-97806200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr9:97790000-97795800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr9:97790000-97796800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr9:97790200-97795600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr9:97790200-97795800	Enhancers	Right Atrium	heart
12	chr9:97790200-97796000	Enhancers	Brain Angular Gyrus	brain
13	chr9:97790200-97796400	Genic enhancers	HSMM	muscle
14	chr9:97790600-97794800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr9:97790600-97795800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr9:97790800-97795600	Genic enhancers	Fetal Intestine Small	intestine
17	chr9:97791200-97795600	Genic enhancers	Liver	Liver
18	chr9:97791200-97795800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr9:97791400-97795800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr9:97791600-97799600	Weak transcription	Hela-S3	cervix
21	chr9:97791600-97800000	Weak transcription	Placenta	Placenta
22	chr9:97791800-97795400	Enhancers	Duodenum Smooth Muscle	Duodenum
23	chr9:97792600-97795800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr9:97792800-97795000	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr9:97792800-97795600	Genic enhancers	Fetal Stomach	stomach
26	chr9:97792800-97795600	Enhancers	Right Ventricle	heart
27	chr9:97792800-97795800	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr9:97792800-97795800	Enhancers	Stomach Mucosa	stomach
29	chr9:97793000-97795800	Enhancers	Brain Cingulate Gyrus	brain
30	chr9:97793000-97795800	Enhancers	Pancreas	Pancrea
31	chr9:97793000-97796000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr9:97793000-97797200	Enhancers	Brain Substantia Nigra	brain
33	chr9:97793000-97800000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr9:97793200-97794800	Enhancers	Brain Germinal Matrix	brain
35	chr9:97793200-97795000	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr9:97793200-97795400	Genic enhancers	Fetal Muscle Leg	muscle
37	chr9:97793200-97795800	Genic enhancers	HSMMtube	muscle
38	chr9:97793200-97796000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr9:97793200-97802200	Weak transcription	Fetal Kidney	kidney
40	chr9:97793400-97795000	Flanking Active TSS	HepG2	liver
41	chr9:97793400-97810400	Weak transcription	HUVEC	blood vessel
42	chr9:97793600-97795200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr9:97793600-97795600	Enhancers	Primary hematopoietic stem cells	blood
44	chr9:97793600-97795600	Enhancers	Fetal Intestine Large	intestine
45	chr9:97793600-97798200	Weak transcription	NHDF-Ad	bronchial
46	chr9:97793800-97795000	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr9:97793800-97795000	Enhancers	Fetal Heart	heart
48	chr9:97793800-97795400	Enhancers	NHEK	skin
49	chr9:97793800-97795600	Enhancers	Duodenum Mucosa	Duodenum
50	chr9:97793800-97795600	Enhancers	Lung	lung

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