Variant report

Variant	rs11830884
Chromosome Location	chr12:49109603-49109604
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:49109426-49111243	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr12:49109580-49111476	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr12:49109595-49111032	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr12:49109224-49111248	HepG2	liver:	n/a	n/a
5	POLR2A	chr12:49108836-49111405	IMR90	lung:	n/a	n/a
6	HCFC1	chr12:49109580-49111678	Hela-S3	cervix:	n/a	n/a
7	GTF3C2	chr12:49109091-49110126	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr12:49109538-49111614	GM12878	blood:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49109119..49112520-chr12:49258264..49261147,4	MCF-7	breast:
2	chr12:49109303..49111589-chr12:49371053..49372870,2	K562	blood:
3	chr12:49103301..49108658-chr12:49108679..49112078,7	K562	blood:
4	chr12:49108930..49110553-chr12:49207843..49209517,2	MCF-7	breast:
5	chr12:49096349..49098245-chr12:49108578..49110236,2	K562	blood:
6	chr12:49072667..49077768-chr12:49107571..49112359,8	MCF-7	breast:
7	chr12:49108937..49110842-chr12:49180917..49183089,2	MCF-7	breast:
8	chr12:49109260..49113049-chr12:49411417..49414170,4	K562	blood:
9	chr12:49109310..49111237-chr12:49657606..49659331,2	K562	blood:
10	chr12:49108385..49110371-chr12:49210566..49212165,2	MCF-7	breast:
11	chr12:49073439..49079132-chr12:49108039..49112179,15	K562	blood:
12	chr12:49072639..49079132-chr12:49108469..49112073,12	K562	blood:
13	chr12:49072707..49077771-chr12:49103757..49111723,15	MCF-7	breast:

No data

Variant related genes	Relation type
CCNT1	TF binding region
ENSG00000174233	Chromatin interaction
ENSG00000125084	Chromatin interaction
ENSG00000181929	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000167535	Chromatin interaction
ENSG00000129315	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000139620	Chromatin interaction
ENSG00000172602	Chromatin interaction
ENSG00000257660	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11168610	1.00[EUR][1000 genomes]
rs11168626	1.00[EUR][1000 genomes]
rs11503892	1.00[EUR][1000 genomes]
rs11534	1.00[EUR][1000 genomes]
rs11551273	1.00[EUR][1000 genomes]
rs11830117	1.00[EUR][1000 genomes]
rs11830164	1.00[EUR][1000 genomes]
rs11831374	1.00[EUR][1000 genomes]
rs11832320	1.00[EUR][1000 genomes]
rs11833394	1.00[EUR][1000 genomes]
rs11833669	1.00[EUR][1000 genomes]
rs11835422	1.00[EUR][1000 genomes]
rs11837122	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11837337	1.00[EUR][1000 genomes]
rs11837993	1.00[EUR][1000 genomes]
rs11838009	0.93[AFR][1000 genomes]
rs11838121	1.00[EUR][1000 genomes]
rs11838289	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11838360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12304826	1.00[EUR][1000 genomes]
rs12305150	1.00[EUR][1000 genomes]
rs12307016	1.00[EUR][1000 genomes]
rs17123267	1.00[EUR][1000 genomes]
rs17123398	1.00[EUR][1000 genomes]
rs2898086	0.90[AFR][1000 genomes]
rs34139009	1.00[EUR][1000 genomes]
rs36119652	1.00[EUR][1000 genomes]
rs55956587	1.00[EUR][1000 genomes]
rs56179964	1.00[EUR][1000 genomes]
rs57337154	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57454425	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57658152	1.00[EUR][1000 genomes]
rs59304927	1.00[EUR][1000 genomes]
rs59636982	1.00[AMR][1000 genomes]
rs59708884	1.00[EUR][1000 genomes]
rs60351852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61663947	1.00[AMR][1000 genomes]
rs71439468	1.00[EUR][1000 genomes]
rs7297499	1.00[AFR][1000 genomes]
rs7303057	1.00[EUR][1000 genomes]
rs7312311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7315319	1.00[EUR][1000 genomes]
rs74088105	0.90[AFR][1000 genomes]
rs74088110	0.90[AFR][1000 genomes]
rs74088131	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74088137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74088149	0.93[AFR][1000 genomes]
rs74088163	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74088167	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74088185	1.00[EUR][1000 genomes]
rs74088186	1.00[EUR][1000 genomes]
rs74089357	1.00[EUR][1000 genomes]
rs74089364	1.00[EUR][1000 genomes]
rs7956989	1.00[EUR][1000 genomes]
rs7959705	1.00[EUR][1000 genomes]
rs7961105	1.00[AMR][1000 genomes]
rs7970421	1.00[EUR][1000 genomes]
rs7973146	1.00[EUR][1000 genomes]
rs7973248	1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3332169	chr12:49005807-49150691	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49107200-49109800	Enhancers	Small Intestine	intestine
2	chr12:49107200-49110400	Transcr. at gene 5' and 3'	Dnd41	blood
3	chr12:49107600-49109800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:49108200-49111600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:49108400-49110000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr12:49108400-49110400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
7	chr12:49108600-49109800	Enhancers	Esophagus	oesophagus
8	chr12:49108600-49110000	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr12:49108600-49110000	Flanking Active TSS	Brain Germinal Matrix	brain
10	chr12:49108600-49111800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr12:49108800-49109800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:49108800-49109800	Enhancers	Spleen	Spleen
13	chr12:49108800-49110000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
14	chr12:49108800-49110000	Flanking Active TSS	Osteobl	bone
15	chr12:49108800-49110400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr12:49108800-49110400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:49108800-49111600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:49108800-49111600	Active TSS	NH-A	brain
19	chr12:49108800-49111600	Active TSS	NHLF	lung
20	chr12:49108800-49111800	Active TSS	iPS-18 Cell Line	embryonic stem cell
21	chr12:49109000-49109800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr12:49109000-49109800	Flanking Active TSS	Liver	Liver
23	chr12:49109000-49110200	Flanking Active TSS	Primary T cells from cord blood	blood
24	chr12:49109000-49110200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr12:49109000-49110200	Active TSS	Right Atrium	heart
26	chr12:49109000-49110200	Flanking Active TSS	Stomach Smooth Muscle	stomach
27	chr12:49109000-49110400	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr12:49109000-49111400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr12:49109000-49111600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:49109000-49111600	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr12:49109000-49111600	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr12:49109000-49111600	Active TSS	Psoas Muscle	Psoas
33	chr12:49109000-49111600	Active TSS	NHDF-Ad	bronchial
34	chr12:49109000-49111800	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr12:49109200-49110000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
36	chr12:49109200-49110000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
37	chr12:49109200-49110000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr12:49109200-49110000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr12:49109200-49110000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
40	chr12:49109200-49110000	Flanking Active TSS	Rectal Smooth Muscle	rectum
41	chr12:49109200-49110200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr12:49109200-49110400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr12:49109200-49111200	Active TSS	Duodenum Mucosa	Duodenum
44	chr12:49109200-49111200	Active TSS	Hela-S3	cervix
45	chr12:49109200-49111200	Active TSS	HMEC	breast
46	chr12:49109200-49111200	Active TSS	HUVEC	blood vessel
47	chr12:49109200-49111200	Active TSS	NHEK	skin
48	chr12:49109200-49111400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr12:49109200-49111400	Active TSS	Fetal Kidney	kidney
50	chr12:49109200-49111400	Active TSS	Right Ventricle	heart

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