Variant report

Variant	rs12069853
Chromosome Location	chr1:10296518-10296519
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:10288684..10290909-chr1:10294452..10296809,3	K562	blood:

Variant related genes	Relation type
ENSG00000054523	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11121543	1.00[CEU][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs11121566	0.83[YRI][hapmap]
rs12064209	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12076005	1.00[CEU][hapmap]
rs12088368	0.89[EUR][1000 genomes]
rs13328720	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4846216	0.94[YRI][hapmap]
rs4846219	0.94[YRI][hapmap]
rs55815752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6703708	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9782879	1.00[CEU][hapmap]
rs9782938	1.00[CEU][hapmap]

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	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv999251	chr1:10276263-10318163	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv545381	chr1:10296452-10423988	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10272600-10368200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:10272800-10296600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:10276800-10311800	Weak transcription	Hela-S3	cervix
4	chr1:10277000-10322000	Weak transcription	Spleen	Spleen
5	chr1:10278400-10302000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:10279800-10297800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:10284800-10311000	Weak transcription	Small Intestine	intestine
8	chr1:10285200-10316000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:10285400-10302400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr1:10285400-10310800	Weak transcription	Aorta	Aorta
11	chr1:10285400-10312600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:10285800-10297000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:10286000-10298000	Weak transcription	Right Atrium	heart
14	chr1:10286000-10301800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr1:10286000-10303000	Weak transcription	Brain Germinal Matrix	brain
16	chr1:10286400-10297000	Weak transcription	HSMMtube	muscle
17	chr1:10286800-10301600	Weak transcription	Fetal Kidney	kidney
18	chr1:10286800-10305800	Weak transcription	Ovary	ovary
19	chr1:10287400-10312400	Weak transcription	Pancreas	Pancrea
20	chr1:10289000-10297200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr1:10289000-10300600	Weak transcription	Fetal Heart	heart
22	chr1:10289200-10301600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr1:10289200-10301800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:10289200-10317400	Weak transcription	Liver	Liver
25	chr1:10289600-10297000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr1:10290400-10296800	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr1:10290600-10299000	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr1:10290800-10297600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:10291000-10311800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:10291000-10311800	Weak transcription	HMEC	breast
31	chr1:10291200-10297200	Weak transcription	Brain Angular Gyrus	brain
32	chr1:10291200-10311200	Weak transcription	HUVEC	blood vessel
33	chr1:10291400-10308600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:10291800-10299600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:10291800-10300800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr1:10292000-10301200	Weak transcription	Esophagus	oesophagus
37	chr1:10292200-10296600	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr1:10292200-10297800	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr1:10292400-10299400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr1:10292400-10299600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr1:10292400-10309400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:10292600-10297000	Weak transcription	NHLF	lung
43	chr1:10292600-10298000	Weak transcription	Psoas Muscle	Psoas
44	chr1:10292600-10299400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:10292600-10303600	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr1:10293000-10296600	Weak transcription	Colon Smooth Muscle	Colon
47	chr1:10293000-10296800	Weak transcription	Adipose Nuclei	Adipose
48	chr1:10293000-10297200	Weak transcription	Primary B cells from peripheral blood	blood
49	chr1:10293000-10322000	Weak transcription	Primary T cells from cord blood	blood
50	chr1:10293200-10296600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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