Variant report

Variant	rs7449629
Chromosome Location	chr6:166798522-166798523
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:166798352-166798532	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:166798420-166798610	MCF10A-Er-Src	breast:	n/a	n/a
3	CEBPB	chr6:166798509-166798853	HepG2	liver:	n/a	chr6:166798671-166798684 chr6:166798673-166798682 chr6:166798673-166798684

No.	Distal block	Cell Line	Cell type
1	chr6:166753320..166757958-chr6:166794622..166799153,8	K562	blood:
2	chr6:166746293..166747904-chr6:166796894..166799021,2	K562	blood:
3	chr6:166743072..166748840-chr6:166793771..166798653,8	K562	blood:
4	chr6:166751804..166757558-chr6:166793969..166799153,5	K562	blood:
5	chr6:166740985..166743870-chr6:166796738..166798607,2	MCF-7	breast:
6	chr6:166796680..166799689-chr6:166808021..166810118,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FGFR1OP-2	chr6:166796964-166802453	NONHSAT116046

Variant related genes	Relation type
MPC1	TF binding region
ENSG00000233231	Chromatin interaction
ENSG00000198818	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1546853	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1546854	0.90[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1546855	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1569459	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1569460	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1569461	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1977049	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1977050	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1977051	0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1977052	0.99[EUR][1000 genomes]
rs1977053	0.97[EUR][1000 genomes]
rs1977054	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1977056	0.89[EUR][1000 genomes]
rs1997661	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2179177	0.94[EUR][1000 genomes]
rs2343591	0.95[CEU][hapmap];0.93[GIH][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3734605	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3757194	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757195	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4305699	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4710043	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456078	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6456079	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6456081	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6902813	0.85[ASN][1000 genomes]
rs6905635	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6906844	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6912695	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6918091	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6918135	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs735297	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7744743	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7752716	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9283865	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295338	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9295341	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295342	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295343	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295344	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9295345	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9348123	0.91[CEU][hapmap];0.86[GIH][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs9348124	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9348125	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9348126	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9355574	0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9355575	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs9356482	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9356483	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9364845	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9364846	0.95[EUR][1000 genomes]
rs9364847	0.95[EUR][1000 genomes]
rs9364848	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9366009	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9366010	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
2	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	nsv523548	chr6:166796433-166819774	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166797400-166801600	Weak transcription	Lung	lung
2	chr6:166797600-166801000	Weak transcription	Adipose Nuclei	Adipose
3	chr6:166797600-166801600	Weak transcription	Brain Germinal Matrix	brain
4	chr6:166797600-166801600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:166797600-166803000	Weak transcription	Brain Substantia Nigra	brain
6	chr6:166797600-166804200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr6:166797600-166808200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr6:166797600-166835800	Weak transcription	Right Atrium	heart
9	chr6:166797800-166801000	Weak transcription	Fetal Intestine Small	intestine
10	chr6:166797800-166801000	Weak transcription	Fetal Lung	lung
11	chr6:166797800-166801200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr6:166797800-166801200	Weak transcription	Fetal Brain Female	brain
13	chr6:166797800-166802200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr6:166797800-166803800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr6:166797800-166804000	Weak transcription	Brain Angular Gyrus	brain
16	chr6:166798000-166799000	Weak transcription	Primary B cells from cord blood	blood
17	chr6:166798000-166801000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:166798000-166801200	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr6:166798000-166801200	Weak transcription	Fetal Intestine Large	intestine
20	chr6:166798000-166802400	Weak transcription	Colon Smooth Muscle	Colon
21	chr6:166798000-166803000	Weak transcription	Pancreas	Pancrea
22	chr6:166798000-166803200	Weak transcription	Fetal Muscle Leg	muscle
23	chr6:166798000-166812200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr6:166798200-166799000	Weak transcription	Liver	Liver
25	chr6:166798200-166800800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:166798200-166801000	Enhancers	HepG2	liver
27	chr6:166798200-166801200	Weak transcription	Monocytes-CD14+_RO01746	blood

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