Variant report

Variant	rs9443654
Chromosome Location	chr6:79949195-79949196
allele	C/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	EP300	chr6:79949145-79949956	GM12878	blood:	n/a	n/a
2	IKZF1	chr6:79949091-79949934	GM12878	blood:	n/a	n/a
3	TBL1XR1	chr6:79949129-79949863	GM12878	blood:	n/a	n/a
4	RELA	chr6:79948942-79949962	GM12878	blood:	n/a	chr6:79949271-79949280 chr6:79949271-79949280
5	RELA	chr6:79949128-79949846	GM19099	blood:	n/a	chr6:79949271-79949280 chr6:79949271-79949280
6	EBF1	chr6:79949133-79949999	GM12878	blood:	n/a	n/a
7	GTF2F1	chr6:79949179-79949439	Hela-S3	cervix:	n/a	n/a
8	RELA	chr6:79949131-79949872	GM18951	blood:	n/a	chr6:79949271-79949280 chr6:79949271-79949280
9	POLR2A	chr6:79948762-79949633	MCF10A-Er-Src	breast:	n/a	n/a
10	EP300	chr6:79949156-79949888	GM12878	blood:	n/a	n/a
11	RCOR1	chr6:79949169-79949952	GM12878	blood:	n/a	n/a
12	BCL11A	chr6:79949149-79949471	GM12878	blood:	n/a	n/a
13	WRNIP1	chr6:79948809-79949938	GM12878	blood:	n/a	n/a
14	CEBPB	chr6:79948634-79949561	Hela-S3	cervix:	n/a	chr6:79948860-79948871
15	RUNX3	chr6:79949156-79950005	GM12878	blood:	n/a	n/a
16	TCF7L2	chr6:79948492-79949478	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:79785425..79789135-chr6:79942833..79950296,12	MCF-7	breast:
2	chr6:79943151..79946532-chr6:79946546..79950345,4	MCF-7	breast:
3	chr6:79943641..79946431-chr6:79946623..79949895,4	MCF-7	breast:
4	chr6:79786599..79788294-chr6:79949135..79951411,2	K562	blood:
5	chr4:6695602..6696103-chr6:79949045..79949545,2	NB4	blood:
6	chr6:79755918..79758564-chr6:79949007..79951329,2	K562	blood:

Variant related genes	Relation type
HMGN3	TF binding region
ENSG00000270362	Chromatin interaction
ENSG00000146247	Chromatin interaction
ENSG00000118418	Chromatin interaction
ENSG00000163993	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10455359	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs10806163	0.84[EUR][1000 genomes]
rs11965180	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11966786	0.97[EUR][1000 genomes]
rs11969279	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12194892	0.84[EUR][1000 genomes]
rs12209677	0.84[EUR][1000 genomes]
rs1335535	1.00[CEU][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1335537	1.00[CEU][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1335538	1.00[CEU][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1414279	0.84[EUR][1000 genomes]
rs1414283	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs1414284	0.94[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1537739	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1537740	1.00[CEU][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1582079	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs16890450	0.84[EUR][1000 genomes]
rs1832088	0.94[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1832089	0.92[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1889685	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2065749	0.82[AFR][1000 genomes]
rs2065750	0.88[AFR][1000 genomes]
rs2095633	0.89[EUR][1000 genomes]
rs2322216	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2322219	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2874732	0.94[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs2874733	0.94[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs3934335	0.92[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs4112504	0.94[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs4235810	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4301272	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4377755	0.94[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs4407672	0.94[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs4418150	0.85[CEU][hapmap];0.95[EUR][1000 genomes]
rs4432946	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4464749	0.94[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs4470813	0.94[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs4537102	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4555887	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4706754	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4706755	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4706756	1.00[CEU][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4706759	1.00[CEU][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4706760	1.00[CEU][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs4706765	1.00[CEU][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs4706766	0.84[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs55635444	0.82[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs56183421	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56193084	0.84[EUR][1000 genomes]
rs56354335	0.84[EUR][1000 genomes]
rs56955811	0.84[EUR][1000 genomes]
rs57340384	0.97[EUR][1000 genomes]
rs57608966	0.84[EUR][1000 genomes]
rs59152048	0.94[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs59858042	0.82[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs61227507	0.82[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs61558200	0.84[EUR][1000 genomes]
rs62411290	0.94[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs6454106	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs6907042	0.82[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs6907264	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6913297	1.00[CEU][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6917165	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6924790	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs6929660	1.00[EUR][1000 genomes]
rs6941433	0.92[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs73468020	0.86[EUR][1000 genomes]
rs73468035	0.84[EUR][1000 genomes]
rs73767530	0.84[EUR][1000 genomes]
rs7738508	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7739118	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7746915	0.88[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7751974	1.00[CEU][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7752593	1.00[CEU][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7757062	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7760458	0.97[EUR][1000 genomes]
rs7760939	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs7763232	0.94[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7764517	0.94[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7770245	0.94[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7772967	0.97[EUR][1000 genomes]
rs9343886	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs9343890	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9350803	1.00[CEU][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9352710	0.86[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs9359369	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs9361504	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs9361511	0.86[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs989191	0.92[YRI][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	nsv830706	chr6:79825910-79994878	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:79944400-79950400	Weak transcription	Lung	lung
2	chr6:79944800-79949200	Weak transcription	HMEC	breast
3	chr6:79944800-79950400	Weak transcription	Right Ventricle	heart
4	chr6:79945000-79955400	Weak transcription	Aorta	Aorta
5	chr6:79947600-79949200	Enhancers	GM12878-XiMat	blood
6	chr6:79947800-79950800	Enhancers	Hela-S3	cervix
7	chr6:79948400-79949200	Enhancers	HepG2	liver
8	chr6:79948400-79949400	Enhancers	Left Ventricle	heart
9	chr6:79948600-79949200	Enhancers	Fetal Intestine Small	intestine
10	chr6:79948600-79949200	Enhancers	Ovary	ovary
11	chr6:79948600-79949400	Enhancers	Pancreas	Pancrea
12	chr6:79948600-79949400	Enhancers	Right Atrium	heart
13	chr6:79948600-79949400	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr6:79948600-79949400	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr6:79948600-79949600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:79948600-79949600	Enhancers	Stomach Mucosa	stomach
17	chr6:79948600-79949600	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr6:79948600-79949800	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr6:79948600-79949800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr6:79948600-79950000	Enhancers	Placenta	Placenta
21	chr6:79948600-79950000	Enhancers	NHEK	skin
22	chr6:79948800-79949200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:79948800-79949400	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr6:79948800-79949400	Enhancers	Gastric	stomach
25	chr6:79948800-79949600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:79948800-79949600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:79948800-79950000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:79949000-79949400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr6:79949000-79949400	Enhancers	Psoas Muscle	Psoas
30	chr6:79949000-79949400	Enhancers	Small Intestine	intestine

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