Variant report

Variant	rs17522849
Chromosome Location	chr12:122231044-122231045
allele	A/C/G
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	TFAP2C	chr12:122229602-122232569	Hela-S3	cervix:	n/a	chr12:122231521-122231536
2	TBL1XR1	chr12:122230771-122231148	GM12878	blood:	n/a	n/a
3	RAD21	chr12:122230746-122231047	GM12878	blood:	n/a	n/a
4	POLR2A	chr12:122229405-122233468	GM19099	blood:	n/a	n/a
5	CEBPD	chr12:122230702-122231115	HepG2	liver:	n/a	n/a
6	SIN3A	chr12:122230765-122231138	GM12878	blood:	n/a	chr12:122230963-122230974
7	POLR2A	chr12:122230884-122231199	HepG2	liver:	n/a	n/a
8	SIN3AK20	chr12:122230934-122233186	PANC-1	pancreas:	n/a	n/a
9	MTA3	chr12:122229860-122233383	GM12878	blood:	n/a	n/a
10	POLR2A	chr12:122229522-122241538	HepG2	liver:	n/a	n/a
11	BCL3	chr12:122229500-122233523	A549	lung:	n/a	chr12:122231001-122231010 chr12:122229915-122229923 chr12:122231561-122231570 chr12:122231384-122231397 chr12:122232267-122232280 chr12:122231383-122231396
12	ZNF143	chr12:122230735-122232535	GM12878	blood:	n/a	chr12:122231317-122231335 chr12:122232277-122232287 chr12:122231181-122231191 chr12:122231312-122231331
13	POLR2A	chr12:122230693-122233942	HepG2	liver:	n/a	n/a
14	POLR2A	chr12:122230263-122231095	GM12892	blood:	n/a	n/a
15	MAZ	chr12:122230686-122233217	GM12878	blood:	n/a	chr12:122231986-122231996 chr12:122231622-122231632
16	CTCF	chr12:122230736-122231098	GM12878	blood:	n/a	n/a
17	ZEB1	chr12:122229267-122233709	HepG2	liver:	n/a	n/a
18	SMARCB1	chr12:122229367-122233602	Hela-S3	cervix:	n/a	chr12:122230186-122230195
19	RELA	chr12:122230737-122232595	GM12891	blood:	n/a	chr12:122231268-122231277 chr12:122231268-122231277
20	CREB1	chr12:122229519-122233581	HepG2	liver:	n/a	n/a
21	MAX	chr12:122230757-122231137	NB4	blood:	n/a	n/a
22	POLR2A	chr12:122229562-122233251	GM18505	blood:	n/a	n/a
23	POLR2A	chr12:122230689-122233658	GM18951	blood:	n/a	n/a
24	TCF12	chr12:122230639-122232666	ECC-1	luminal epithelium:	n/a	chr12:122231871-122231881 chr12:122232576-122232586
25	RCOR1	chr12:122230354-122231060	GM12878	blood:	n/a	n/a
26	POLR2A	chr12:122230935-122231759	GM12891	blood:	n/a	n/a
27	FOXM1	chr12:122230692-122231118	GM12878	blood:	n/a	n/a
28	MYC	chr12:122230687-122231215	NB4	blood:	n/a	n/a
29	NR2F2	chr12:122230629-122232685	MCF-7	breast:	n/a	n/a
30	POLR2A	chr12:122230834-122233194	HCT-116	colon:	n/a	n/a
31	POLR2A	chr12:122230552-122233270	GM15510	blood:	n/a	n/a
32	POLR2A	chr12:122230384-122234714	ECC-1	luminal epithelium:	n/a	n/a
33	POLR2A	chr12:122229543-122233541	GM12892	blood:	n/a	n/a
34	MAX	chr12:122229426-122233619	A549	lung:	n/a	chr12:122231986-122231996 chr12:122231622-122231632
35	ZBTB7A	chr12:122230715-122232576	ECC-1	luminal epithelium:	n/a	chr12:122231357-122231364 chr12:122232504-122232518 chr12:122231029-122231037 chr12:122231278-122231287
36	POLR2A	chr12:122229221-122241674	GM12892	blood:	n/a	n/a
37	PAX5	chr12:122230937-122231249	GM12878	blood:	n/a	n/a
38	MAX	chr12:122230759-122231185	GM12878	blood:	n/a	n/a
39	POLR2A	chr12:122230603-122234670	GM12892	blood:	n/a	n/a
40	NRF1	chr12:122230914-122231083	H1-hESC	embryonic stem cell:	n/a	chr12:122231038-122231052 chr12:122231041-122231055 chr12:122231041-122231050 chr12:122231041-122231052
41	POLR2A	chr12:122230973-122231187	A549	lung:	n/a	n/a
42	POLR2A	chr12:122230545-122233420	GM12891	blood:	n/a	n/a
43	ELF1	chr12:122230114-122232430	GM12878	blood:	n/a	chr12:122231641-122231653 chr12:122231543-122231555 chr12:122231560-122231569 chr12:122231645-122231654 chr12:122232275-122232287
44	PML	chr12:122229506-122233753	GM12878	blood:	n/a	n/a
45	CREB1	chr12:122230674-122231307	A549	lung:	n/a	n/a
46	POLR2A	chr12:122230769-122231258	HepG2	liver:	n/a	n/a
47	RELA	chr12:122230708-122233213	GM15510	blood:	n/a	chr12:122231268-122231277 chr12:122231268-122231277
48	MAX	chr12:122230944-122231090	HepG2	liver:	n/a	n/a
49	TCF12	chr12:122229223-122233557	A549	lung:	n/a	chr12:122233009-122233019 chr12:122231871-122231881 chr12:122232576-122232586
50	SP1	chr12:122229479-122231264	A549	lung:	n/a	chr12:122231007-122231020 chr12:122230029-122230036 chr12:122229855-122229865

No.	Distal block	Cell Line	Cell type
1	chr12:122230934..122233822-chr12:122459500..122463009,3	MCF-7	breast:
2	chr12:122015890..122017624-chr12:122230329..122231836,2	MCF-7	breast:
3	chr12:122228992..122246947-chr12:122322343..122339116,70	MCF-7	breast:
4	chr12:122149249..122152147-chr12:122229581..122233327,7	MCF-7	breast:
5	chr12:116997056..116999076-chr12:122230249..122232872,2	K562	blood:
6	chr12:122228836..122242951-chr12:122324438..122335797,34	K562	blood:
7	chr12:122188669..122193873-chr12:122227176..122233304,8	MCF-7	breast:
8	chr12:122230934..122231621-chr19:39926580..39927261,2	Hela-S3	cervix:
9	chr12:122228999..122246158-chr12:122324401..122342013,93	MCF-7	breast:
10	chr12:120727170..120730056-chr12:122229573..122231675,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272849	TF binding region
ENSG00000256950	Chromatin interaction
ENSG00000171471	Chromatin interaction
ENSG00000110987	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000105193	Chromatin interaction
ENSG00000089094	Chromatin interaction
ENSG00000188735	Chromatin interaction
ENSG00000110801	Chromatin interaction
ENSG00000196235	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12229133	1.00[AFR][1000 genomes]
rs36023382	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3741594	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3809143	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58801491	1.00[ASN][1000 genomes]
rs59912940	0.93[ASN][1000 genomes]
rs61736010	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61743641	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv899566	chr12:122167095-122265106	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
3	nsv899567	chr12:122203680-122281575	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv984477	chr12:122226309-122271532	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122211600-122231200	Weak transcription	Brain Hippocampus Middle	brain
2	chr12:122211800-122231600	Weak transcription	Brain Substantia Nigra	brain
3	chr12:122223200-122231400	Weak transcription	HSMM	muscle
4	chr12:122224600-122231200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr12:122225200-122231400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr12:122225800-122233200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr12:122227200-122231600	Weak transcription	K562	blood
8	chr12:122227400-122232000	Active TSS	Rectal Smooth Muscle	rectum
9	chr12:122228400-122231200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr12:122228600-122232400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:122229200-122231400	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr12:122229200-122232200	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr12:122229400-122231400	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr12:122229400-122231400	Enhancers	HMEC	breast
15	chr12:122229400-122232000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
16	chr12:122229400-122232200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
17	chr12:122229400-122232400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
18	chr12:122229400-122233000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:122229400-122233000	Flanking Active TSS	Duodenum Mucosa	Duodenum
20	chr12:122229600-122231200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:122229600-122231200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr12:122229600-122231200	Enhancers	NHEK	skin
23	chr12:122229600-122235400	Enhancers	Fetal Heart	heart
24	chr12:122229800-122231200	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
25	chr12:122229800-122233000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:122230000-122231200	Flanking Active TSS	Spleen	Spleen
27	chr12:122230000-122231800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr12:122230000-122233200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr12:122230200-122231200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
30	chr12:122230200-122231400	Active TSS	Liver	Liver
31	chr12:122230200-122231600	Weak transcription	HSMMtube	muscle
32	chr12:122230200-122231800	Active TSS	Esophagus	oesophagus
33	chr12:122230200-122232200	Flanking Active TSS	Placenta	Placenta
34	chr12:122230200-122233000	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr12:122230200-122233000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
36	chr12:122230400-122231200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr12:122230400-122231200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr12:122230400-122231200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
39	chr12:122230400-122231200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr12:122230400-122231200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr12:122230400-122231600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr12:122230400-122231800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr12:122230400-122231800	Active TSS	Brain Cingulate Gyrus	brain
44	chr12:122230400-122231800	Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr12:122230400-122232000	Active TSS	Left Ventricle	heart
46	chr12:122230400-122232000	Active TSS	Small Intestine	intestine
47	chr12:122230400-122232000	Flanking Active TSS	Stomach Mucosa	stomach
48	chr12:122230400-122232400	Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr12:122230400-122232800	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr12:122230600-122231200	Flanking Active TSS	Colon Smooth Muscle	Colon

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