Variant report

Variant	rs11537654
Chromosome Location	chr12:57985204-57985205
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57983190..57986031-chr12:58086563..58089648,3	K562	blood:
2	chr12:57919943..57923943-chr12:57984305..57987540,4	MCF-7	breast:
3	chr12:57914619..57916153-chr12:57984112..57986210,2	K562	blood:
4	chr12:57984280..57986133-chr12:58130711..58132725,2	K562	blood:
5	chr12:57983454..57989400-chr12:57989791..58002327,29	MCF-7	breast:
6	chr12:57912627..57914339-chr12:57984799..57986574,2	MCF-7	breast:
7	chr12:57983103..57986007-chr12:58086180..58089172,2	MCF-7	breast:
8	chr12:57984859..57985397-chr19:55896847..55897561,2	HCT-116	colon:
9	chr12:49658553..49659361-chr12:57984439..57985376,2	Hela-S3	cervix:
10	chr12:57984405..57986520-chr12:58117809..58119763,2	MCF-7	breast:
11	chr12:57983953..57986282-chr12:58144732..58146492,2	K562	blood:
12	chr12:57983992..57986489-chr12:58138776..58141177,2	MCF-7	breast:
13	chr12:57983862..57986521-chr12:58113615..58115210,2	MCF-7	breast:
14	chr12:57983573..57987941-chr12:58024849..58028209,5	MCF-7	breast:
15	chr12:57916409..57919050-chr12:57983099..57985919,3	MCF-7	breast:
16	chr12:57985035..57986943-chr12:58137813..58139906,2	K562	blood:
17	chr12:57940234..57941945-chr12:57983939..57986632,2	MCF-7	breast:
18	chr12:57939429..57943777-chr12:57984797..57987088,3	K562	blood:
19	chr1:211431871..211432822-chr12:57984812..57985355,2	Hela-S3	cervix:
20	chr12:57984385..57986376-chr12:58138351..58140314,2	K562	blood:
21	chr12:57983656..57985947-chr12:58119170..58122047,3	MCF-7	breast:
22	chr12:57942322..57945252-chr12:57983891..57986391,2	MCF-7	breast:
23	chr12:57869564..57871597-chr12:57983396..57986014,2	K562	blood:
24	chr12:57983700..57986584-chr12:58162901..58165594,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000175203	Chromatin interaction
ENSG00000117625	Chromatin interaction
ENSG00000123329	Chromatin interaction
ENSG00000135452	Chromatin interaction
ENSG00000123427	Chromatin interaction
ENSG00000037897	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000135506	Chromatin interaction
ENSG00000135439	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000135446	Chromatin interaction
ENSG00000155980	Chromatin interaction
ENSG00000257499	Chromatin interaction
ENSG00000166908	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000178498	Chromatin interaction
ENSG00000255737	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000135454	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1545783	0.89[JPT][hapmap]
rs2306390	1.00[ASW][hapmap];0.91[CEU][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2888334	0.91[CEU][hapmap]
rs4760158	0.89[JPT][hapmap]
rs775251	0.91[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1812398	chr12:57829733-58001868	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv2758310	chr12:57829733-58001868	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	esv2759901	chr12:57829733-58001868	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	nsv428283	chr12:57829733-58001868	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
6	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
7	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
8	nsv541504	chr12:57958701-58062311	Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv725	chr12:57966549-57993808	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	n/a

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs11537654	HOXC5	cis	cerebellum	SCAN
rs11537654	ITGB7	cis	cerebellum	SCAN
rs11537654	ESPL1	cis	parietal	SCAN
rs11537654	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs11537654	TSPAN31	cis	cerebellum	SCAN
rs11537654	KIAA0748	cis	cerebellum	SCAN
rs11537654	FAM119B	cis	lymphoblastoid	seeQTL
rs11537654	CDK4	cis	cerebellum	SCAN
rs11537654	FAM119B	cis	cerebellum	SCAN
rs11537654	TSPAN31	cis	parietal	SCAN
rs11537654	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs11537654	STAT6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57984000-57986400	Flanking Active TSS	Dnd41	blood
2	chr12:57984200-57985600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:57984200-57985600	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr12:57984200-57985600	Active TSS	A549	lung
5	chr12:57984200-57985800	Active TSS	H9 Cell Line	embryonic stem cell
6	chr12:57984200-57985800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:57984200-57985800	Active TSS	Rectal Smooth Muscle	rectum
8	chr12:57984200-57986000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr12:57984200-57986200	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr12:57984200-57986200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
11	chr12:57984200-57986200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:57984200-57986200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:57984200-57986400	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr12:57984400-57985400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:57984400-57985400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:57984400-57985600	Flanking Active TSS	Primary hematopoietic stem cells	blood
17	chr12:57984400-57985600	Active TSS	Placenta Amnion	Placenta Amnion
18	chr12:57984400-57985800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr12:57984400-57985800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr12:57984400-57985800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr12:57984400-57985800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
22	chr12:57984400-57985800	Active TSS	Aorta	Aorta
23	chr12:57984400-57985800	Active TSS	HSMMtube	muscle
24	chr12:57984400-57986000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:57984400-57986000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr12:57984600-57985400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr12:57984600-57985400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
28	chr12:57984600-57985400	Active TSS	HSMM	muscle
29	chr12:57984600-57985600	Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr12:57984600-57985600	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr12:57984600-57985600	Active TSS	Brain Angular Gyrus	brain
32	chr12:57984600-57985600	Active TSS	Psoas Muscle	Psoas
33	chr12:57984600-57985600	Active TSS	Sigmoid Colon	Sigmoid Colon
34	chr12:57984600-57985800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr12:57984600-57985800	Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr12:57984600-57985800	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr12:57984600-57985800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:57984600-57985800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr12:57984600-57985800	Active TSS	Gastric	stomach
40	chr12:57984600-57985800	Active TSS	Left Ventricle	heart
41	chr12:57984600-57985800	Active TSS	Ovary	ovary
42	chr12:57984600-57985800	Active TSS	Pancreas	Pancrea
43	chr12:57984600-57985800	Active TSS	Right Atrium	heart
44	chr12:57984600-57985800	Active TSS	Right Ventricle	heart
45	chr12:57984600-57985800	Active TSS	Small Intestine	intestine
46	chr12:57984600-57986000	Active TSS	Esophagus	oesophagus
47	chr12:57984600-57986000	Active TSS	Fetal Intestine Small	intestine
48	chr12:57984600-57986200	Active TSS	Brain Hippocampus Middle	brain
49	chr12:57984600-57986200	Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr12:57984600-57987000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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