Variant report

Variant	rs2250989
Chromosome Location	chr6:76002563-76002564
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:75952125..75954686-chr6:76000719..76002598,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FILIP1-1	chr6:76001574-76003213	NONHSAT113604

Variant related genes	Relation type
ENSG00000112695	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1018471	1.00[ASW][hapmap];0.84[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10806035	0.84[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13220419	0.90[GIH][hapmap]
rs171263	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs240374	0.83[ASW][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap]
rs240375	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs240378	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs240379	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs240380	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2748252	1.00[ASW][hapmap];0.92[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2808201	0.80[CEU][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap]
rs2808203	0.80[CEU][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs2842445	0.86[EUR][1000 genomes]
rs2842446	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2842458	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2842459	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2842461	0.90[GIH][hapmap]
rs2842462	1.00[ASW][hapmap];0.84[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2842463	1.00[ASW][hapmap];0.84[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4275021	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs4374801	0.80[CEU][hapmap]
rs4412169	0.80[EUR][1000 genomes]
rs4708179	0.84[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs502900	0.90[GIH][hapmap]
rs6903526	0.80[CEU][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs6904580	0.80[CEU][hapmap];0.80[GIH][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs6929270	0.80[CEU][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs7743227	0.88[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7771904	0.80[CEU][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs7772989	0.90[JPT][hapmap]
rs9341515	0.81[EUR][1000 genomes]
rs9343283	0.82[EUR][1000 genomes]
rs9352202	0.84[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9359122	0.80[CEU][hapmap];0.80[GIH][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016804	chr6:75775846-76188585	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538310	chr6:75775846-76188585	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1024079	chr6:75848556-76238519	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1027915	chr6:75893542-76510113	Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
5	nsv538311	chr6:75893542-76510113	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
6	nsv603763	chr6:75923605-76009426	Genic enhancers Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv603764	chr6:75963751-76025603	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv830698	chr6:75968810-76115592	Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2250989	TMEM30A	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:75995200-76010000	Weak transcription	Lung	lung
2	chr6:75995200-76016800	Weak transcription	Left Ventricle	heart
3	chr6:75995400-76021800	Weak transcription	Right Ventricle	heart
4	chr6:75995400-76027600	Weak transcription	Aorta	Aorta
5	chr6:75995600-76009600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:75995800-76002600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr6:75995800-76002800	Weak transcription	Fetal Intestine Small	intestine
8	chr6:75995800-76009000	Weak transcription	Colon Smooth Muscle	Colon
9	chr6:75995800-76009600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:75995800-76009600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:75995800-76009600	Weak transcription	Fetal Muscle Leg	muscle
12	chr6:75995800-76009600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr6:75995800-76009800	Weak transcription	Fetal Heart	heart
14	chr6:75995800-76018200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr6:75995800-76027200	Weak transcription	Fetal Stomach	stomach
16	chr6:75996000-76002600	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr6:75996000-76002800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:75996000-76003200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:75996000-76004000	Weak transcription	Esophagus	oesophagus
20	chr6:75996000-76009800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr6:75996000-76022600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr6:75996200-76009800	Weak transcription	Small Intestine	intestine
23	chr6:75996400-76004000	Weak transcription	Primary T cells from cord blood	blood
24	chr6:75996400-76007400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr6:75996400-76009800	Weak transcription	Adipose Nuclei	Adipose
26	chr6:75997600-76009600	Weak transcription	Liver	Liver
27	chr6:75997800-76009800	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr6:75998400-76010000	Weak transcription	Placenta	Placenta
29	chr6:76000000-76009200	Weak transcription	Fetal Lung	lung
30	chr6:76000600-76009200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr6:76001000-76009600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr6:76001400-76009200	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr6:76001400-76009800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr6:76001400-76011800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr6:76001600-76003000	Weak transcription	Brain Hippocampus Middle	brain
36	chr6:76001600-76009800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr6:76002200-76002600	Enhancers	Brain Anterior Caudate	brain
38	chr6:76002400-76002600	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr6:76002400-76002600	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr6:76002400-76003600	Weak transcription	GM12878-XiMat	blood

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