Variant report

Variant	rs6779476
Chromosome Location	chr3:24002218-24002219
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:24002152-24002870	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:23958060..23960570-chr3:24001366..24003390,2	MCF-7	breast:
2	chr3:23961452..23965156-chr3:23999587..24004253,5	MCF-7	breast:
3	chr3:23985538..23993367-chr3:23993730..24003801,19	MCF-7	breast:
4	chr3:23967304..23969953-chr3:24001242..24004073,2	K562	blood:
5	chr3:23967043..23969562-chr3:24002136..24003656,2	MCF-7	breast:

No data

Variant related genes	Relation type
NR1D2	TF binding region
ENSG00000174738	Chromatin interaction
ENSG00000174748	Chromatin interaction
ENSG00000197885	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10865791	0.95[CHB][hapmap]
rs11129130	0.95[CHB][hapmap]
rs11717862	0.97[EUR][1000 genomes]
rs12631785	0.83[CEU][hapmap]
rs13091509	0.88[EUR][1000 genomes]
rs13095392	0.92[CEU][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1567582	0.86[ASN][1000 genomes]
rs4025822	0.81[EUR][1000 genomes]
rs4078155	0.95[CHB][hapmap]
rs4131403	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4241514	0.85[EUR][1000 genomes]
rs4241515	0.81[EUR][1000 genomes]
rs4241517	0.92[CEU][hapmap];0.86[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs4241520	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4292186	0.95[CHB][hapmap]
rs4293661	0.95[CHB][hapmap]
rs4321479	0.96[CEU][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4578971	0.95[CHB][hapmap]
rs4589882	0.96[CEU][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4619734	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4858094	0.87[CEU][hapmap];0.81[GIH][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs4858095	0.96[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4858098	0.96[CEU][hapmap];0.98[EUR][1000 genomes]
rs4858551	0.83[EUR][1000 genomes]
rs4858553	0.87[CEU][hapmap];0.81[GIH][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs4858561	0.95[CHB][hapmap]
rs4858565	0.89[EUR][1000 genomes]
rs4858567	0.96[CEU][hapmap];0.91[GIH][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs4858569	0.84[CEU][hapmap];0.85[TSI][hapmap]
rs5023610	0.96[CEU][hapmap]
rs62253379	0.89[EUR][1000 genomes]
rs6419846	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6550815	0.94[EUR][1000 genomes]
rs6550819	0.92[EUR][1000 genomes]
rs6550823	0.96[CEU][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6550824	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6550825	0.85[ASN][1000 genomes]
rs6550826	0.87[ASN][1000 genomes]
rs6550828	0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.87[ASN][1000 genomes]
rs6764154	0.83[EUR][1000 genomes]
rs6778783	0.85[EUR][1000 genomes]
rs6790557	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6793391	0.80[EUR][1000 genomes]
rs6794922	0.96[CEU][hapmap];0.95[GIH][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6800790	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs6807856	0.84[CEU][hapmap];0.90[TSI][hapmap]
rs7371944	0.92[CEU][hapmap];0.87[GIH][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7431301	0.98[EUR][1000 genomes]
rs7615255	0.83[CEU][hapmap];0.81[GIH][hapmap];0.84[TSI][hapmap]
rs7619870	0.96[ASN][1000 genomes]
rs7626431	0.83[CEU][hapmap]
rs7631236	0.92[ASN][1000 genomes]
rs7636810	0.80[CEU][hapmap];0.90[TSI][hapmap]
rs7646930	0.95[CHB][hapmap]
rs7651185	0.84[TSI][hapmap]
rs9310725	0.83[EUR][1000 genomes]
rs9831760	0.95[CHB][hapmap]
rs9842907	0.82[CEU][hapmap]
rs9845287	0.87[CEU][hapmap];0.81[GIH][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs9863320	0.81[EUR][1000 genomes]
rs9879378	0.82[EUR][1000 genomes]
rs9882735	0.97[EUR][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	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv834638	chr3:23963860-24117191	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23988200-24003600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:23988400-24003000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr3:23988400-24003400	Weak transcription	Fetal Kidney	kidney
4	chr3:23989200-24003000	Weak transcription	Fetal Thymus	thymus
5	chr3:23989200-24007400	Weak transcription	Fetal Brain Female	brain
6	chr3:23989200-24018000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:23989200-24020600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:23989200-24033200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr3:23989600-24003400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:23989600-24003400	Weak transcription	Esophagus	oesophagus
11	chr3:23989600-24003600	Weak transcription	Colonic Mucosa	Colon
12	chr3:23989800-24017800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:23992000-24007400	Weak transcription	Thymus	Thymus
14	chr3:23992400-24002400	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr3:23992400-24003400	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr3:23992400-24003400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr3:23992400-24003400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:23992400-24017400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr3:23993600-24009400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr3:23993600-24017800	Weak transcription	Brain Germinal Matrix	brain
21	chr3:23994000-24022800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:23995200-24003200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr3:23995200-24003200	Weak transcription	Dnd41	blood
24	chr3:23995200-24003400	Weak transcription	GM12878-XiMat	blood
25	chr3:23995600-24003200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr3:23995800-24003000	Weak transcription	HepG2	liver
27	chr3:23996000-24012600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr3:23996200-24004800	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr3:23996200-24009400	Weak transcription	Psoas Muscle	Psoas
30	chr3:23996200-24011200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:23996200-24021200	Weak transcription	Small Intestine	intestine
32	chr3:23996400-24006200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr3:23996800-24003000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr3:23996800-24003000	Weak transcription	Right Ventricle	heart
35	chr3:23996800-24003200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr3:23997200-24012200	Strong transcription	Liver	Liver
37	chr3:23997400-24007400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr3:23998200-24003600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr3:23998400-24003400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:23999000-24007400	Strong transcription	Adipose Nuclei	Adipose
41	chr3:23999200-24011600	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr3:23999400-24002600	Enhancers	Stomach Mucosa	stomach
43	chr3:23999400-24005000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr3:23999400-24005000	Strong transcription	Fetal Lung	lung
45	chr3:23999800-24003000	Weak transcription	Spleen	Spleen
46	chr3:23999800-24019600	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr3:24000000-24002400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr3:24000000-24002800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:24000000-24003400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr3:24000000-24007400	Weak transcription	Right Atrium	heart

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