Variant report

Variant	rs6660575
Chromosome Location	chr1:170430955-170430956
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KIFAP3-2	chr1:170430458-170431560	ENSG00000231407.1
2	lnc-KIFAP3-2	chr1:170429594-170431560	ENSG00000231407.1
3	lnc-KIFAP3-2	chr1:170429594-170431560	NONHSAT007498

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10157476	0.81[AFR][1000 genomes]
rs10733056	0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10753810	0.82[AFR][1000 genomes]
rs10753811	0.81[AFR][1000 genomes]
rs10753814	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10753815	0.90[ASW][hapmap];0.90[LWK][hapmap];0.95[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10800527	0.91[LWK][hapmap];0.90[MKK][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes]
rs10919393	0.81[AFR][1000 genomes]
rs10919425	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10919434	1.00[AMR][1000 genomes]
rs12062348	1.00[AMR][1000 genomes]
rs12072089	1.00[AMR][1000 genomes]
rs12087798	1.00[AMR][1000 genomes]
rs12088253	1.00[AMR][1000 genomes]
rs12116909	0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1333133	0.90[ASW][hapmap];0.94[LWK][hapmap];0.95[MKK][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1333142	0.91[YRI][hapmap]
rs1333146	0.83[AFR][1000 genomes]
rs1333150	0.91[AFR][1000 genomes]
rs1333151	0.85[AFR][1000 genomes]
rs1333152	0.81[AFR][1000 genomes]
rs1333153	0.85[AFR][1000 genomes]
rs1333154	0.85[AFR][1000 genomes]
rs1333155	0.97[AFR][1000 genomes]
rs1333156	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1412891	0.83[AFR][1000 genomes]
rs1412892	0.91[YRI][hapmap];0.89[AFR][1000 genomes]
rs1412893	0.89[AFR][1000 genomes]
rs1412894	0.81[AFR][1000 genomes]
rs1412895	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1537390	0.91[YRI][hapmap]
rs1537395	0.83[YRI][hapmap];0.83[AFR][1000 genomes]
rs1537397	0.90[ASW][hapmap];0.90[LWK][hapmap];0.95[MKK][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1572026	0.85[AFR][1000 genomes]
rs1572027	0.83[AFR][1000 genomes]
rs1576979	0.84[AFR][1000 genomes]
rs1576980	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1831756	0.85[AFR][1000 genomes]
rs1855221	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1928716	0.91[YRI][hapmap]
rs1930632	0.89[MKK][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes]
rs1930633	0.85[AFR][1000 genomes]
rs1930634	0.85[AFR][1000 genomes]
rs1970116	0.81[AFR][1000 genomes]
rs2104918	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2150029	0.90[ASW][hapmap];0.90[LWK][hapmap];0.95[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2151333	0.82[AFR][1000 genomes]
rs2225322	0.90[ASW][hapmap];0.90[LWK][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2421325	0.88[LWK][hapmap];0.85[MKK][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes]
rs2901401	0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3936919	0.83[AFR][1000 genomes]
rs3980839	0.91[AFR][1000 genomes]
rs4233350	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4325194	0.89[AFR][1000 genomes]
rs4402174	0.95[AFR][1000 genomes]
rs4415629	0.89[AFR][1000 genomes]
rs4436439	0.81[AFR][1000 genomes]
rs4469769	0.85[AFR][1000 genomes]
rs4603185	0.82[AFR][1000 genomes]
rs4656769	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4656771	0.83[AFR][1000 genomes]
rs4656775	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4656777	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4656779	1.00[ASW][hapmap];0.97[LWK][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4656783	0.90[AFR][1000 genomes]
rs57462154	1.00[AMR][1000 genomes]
rs57674813	1.00[AMR][1000 genomes]
rs6427248	0.86[AFR][1000 genomes]
rs6427249	0.86[AFR][1000 genomes]
rs6427255	0.85[AFR][1000 genomes]
rs6427260	0.88[LWK][hapmap];0.90[MKK][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes]
rs6427261	0.91[LWK][hapmap];0.90[MKK][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes]
rs6657164	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6664037	0.90[YRI][hapmap];0.91[AFR][1000 genomes]
rs6667304	0.92[AFR][1000 genomes]
rs6669308	0.91[LWK][hapmap];0.90[MKK][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes]
rs6670724	0.99[AFR][1000 genomes]
rs6671312	0.91[YRI][hapmap];0.89[AFR][1000 genomes]
rs6676081	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6680083	1.00[AMR][1000 genomes]
rs6693763	0.91[LWK][hapmap];0.85[MKK][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes]
rs6698637	0.82[AFR][1000 genomes]
rs6699057	0.82[AFR][1000 genomes]
rs6701004	0.85[AFR][1000 genomes]
rs6701218	0.87[YRI][hapmap];0.90[AFR][1000 genomes]
rs6703801	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7523665	0.88[AFR][1000 genomes]
rs7531125	0.90[ASW][hapmap];0.90[LWK][hapmap];0.95[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7538125	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7548443	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7553254	0.91[YRI][hapmap];0.89[AFR][1000 genomes]
rs9651042	0.82[AFR][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	nsv1014033	chr1:169968488-170453021	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535200	chr1:169968488-170453021	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	nsv872543	chr1:170171083-170674903	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv533915	chr1:170258766-170725296	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:170429000-170432200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr1:170429200-170432200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:170429400-170431800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:170429400-170431800	Enhancers	Dnd41	blood
5	chr1:170429600-170431600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:170430000-170431400	Enhancers	NHLF	lung
7	chr1:170430000-170431600	Enhancers	NHDF-Ad	bronchial
8	chr1:170430200-170431600	Enhancers	NH-A	brain
9	chr1:170430200-170431800	Enhancers	Muscle Satellite Cultured Cells	--
10	chr1:170430400-170431600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:170430400-170431600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr1:170430600-170431000	Enhancers	Placenta Amnion	Placenta Amnion
13	chr1:170430600-170431400	Flanking Active TSS	HSMM	muscle
14	chr1:170430600-170431600	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr1:170430600-170431600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:170430600-170431600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:170430600-170431600	Enhancers	Fetal Muscle Leg	muscle
18	chr1:170430800-170431200	Flanking Active TSS	Osteobl	bone
19	chr1:170430800-170431600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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