Variant report

Variant	rs685862
Chromosome Location	chr1:47135955-47135956
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr1:47135838-47136215	K562	blood:	n/a	n/a
2	BACH1	chr1:47135861-47136125	K562	blood:	n/a	n/a
3	MAFF	chr1:47135810-47136164	K562	blood:	n/a	n/a
4	MAFK	chr1:47135800-47136143	K562	blood:	n/a	n/a
5	JUND	chr1:47135676-47136293	K562	blood:	n/a	n/a
6	STAT3	chr1:47135903-47136032	MCF10A-Er-Src	breast:	n/a	n/a
7	EGR1	chr1:47135777-47135997	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:47131887..47139340-chr1:47181784..47186573,11	K562	blood:
2	chr1:47133847..47136859-chr1:47183270..47186412,3	K562	blood:
3	chr1:47079661..47082285-chr1:47135813..47137705,2	K562	blood:
4	chr1:47134358..47137339-chr1:47183387..47185827,2	MCF-7	breast:
5	chr1:47133631..47136554-chr1:47137710..47141962,4	K562	blood:
6	chr1:47130612..47137538-chr1:47138503..47143012,9	K562	blood:
7	chr1:47108263..47110461-chr1:47134867..47136789,2	K562	blood:
8	chr1:47134378..47137611-chr1:47139710..47142903,4	MCF-7	breast:
9	chr1:47134287..47136852-chr1:47138117..47139620,2	MCF-7	breast:

No data

Variant related genes	Relation type
EFCAB14-AS1	TF binding region
ATPAF1	TF binding region
ENSG00000233647	TF binding region
TEX38	TF binding region
ENSG00000159658	Chromatin interaction
ENSG00000142961	Chromatin interaction
ENSG00000228237	Chromatin interaction
ENSG00000123472	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10890410	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11211343	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11801744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12059860	1.00[CEU][hapmap]
rs12566278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1258055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1258058	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1258064	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1258065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1258066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1258072	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes]
rs1273237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13374909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1933932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs2241863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs2241864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs2476155	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2476159	0.85[AMR][1000 genomes]
rs3766218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3766220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs3766221	0.95[AMR][1000 genomes]
rs3766222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3766223	1.00[CHB][hapmap];0.85[AMR][1000 genomes]
rs57495753	0.84[AMR][1000 genomes]
rs583649	0.95[AMR][1000 genomes]
rs58678760	0.85[AMR][1000 genomes]
rs604233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs604264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes]
rs629412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs631368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs631840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs636082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs636122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs636424	0.95[AMR][1000 genomes]
rs655369	0.95[AMR][1000 genomes]
rs6677350	1.00[CEU][hapmap]
rs669647	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes]
rs678466	0.84[AMR][1000 genomes]
rs723333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs724309	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap]
rs736188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][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	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription 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 target site	32 gene(s)	inside rSNPs	diseases
3	nsv1013048	chr1:47132831-47377364	Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv534955	chr1:47132831-47377364	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47134400-47136600	Enhancers	K562	blood
2	chr1:47134400-47140400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:47134400-47145800	Weak transcription	Hela-S3	cervix
4	chr1:47134400-47147800	Weak transcription	Small Intestine	intestine
5	chr1:47134600-47137600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:47134600-47138000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:47134600-47138000	Weak transcription	Fetal Heart	heart
8	chr1:47134600-47138200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:47134600-47138200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:47134600-47138200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr1:47134600-47138200	Weak transcription	Gastric	stomach
12	chr1:47134600-47138200	Weak transcription	Thymus	Thymus
13	chr1:47134600-47138400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr1:47134600-47138600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr1:47134600-47138600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:47134600-47138600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr1:47134600-47138800	Weak transcription	Primary B cells from cord blood	blood
18	chr1:47134600-47138800	Weak transcription	Fetal Muscle Leg	muscle
19	chr1:47134600-47139000	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr1:47134600-47139000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr1:47134600-47139200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:47134600-47139200	Weak transcription	Primary B cells from peripheral blood	blood
23	chr1:47134600-47139200	Weak transcription	Brain Germinal Matrix	brain
24	chr1:47134600-47139200	Weak transcription	Fetal Brain Female	brain
25	chr1:47134600-47139400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:47134600-47139400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:47134600-47139400	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr1:47134600-47139400	Weak transcription	Liver	Liver
29	chr1:47134600-47139400	Weak transcription	Left Ventricle	heart
30	chr1:47134600-47139600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr1:47134600-47139600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:47134600-47139600	Weak transcription	Stomach Mucosa	stomach
33	chr1:47134600-47139600	Weak transcription	HSMM	muscle
34	chr1:47134600-47139600	Weak transcription	Osteobl	bone
35	chr1:47134600-47139800	Weak transcription	NHLF	lung
36	chr1:47134600-47140800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr1:47134600-47141200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr1:47134600-47141200	Weak transcription	Aorta	Aorta
39	chr1:47134600-47141200	Weak transcription	HepG2	liver
40	chr1:47134600-47141400	Weak transcription	NH-A	brain
41	chr1:47134600-47142600	Weak transcription	HSMMtube	muscle
42	chr1:47134600-47142800	Weak transcription	Ovary	ovary
43	chr1:47134600-47143000	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr1:47134600-47143200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:47134600-47145600	Weak transcription	Fetal Kidney	kidney
46	chr1:47134600-47145800	Weak transcription	Fetal Brain Male	brain
47	chr1:47134600-47147000	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr1:47134600-47147800	Weak transcription	Psoas Muscle	Psoas
49	chr1:47134600-47149200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr1:47134600-47153000	Weak transcription	Right Atrium	heart

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