Variant report

Variant	rs11188518
Chromosome Location	chr10:97666798-97666799
allele	G/T
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	CTCF	chr10:97666780-97666930	HFF	foreskin:	n/a	n/a
2	YY1	chr10:97666748-97666949	K562	blood:	n/a	n/a
3	CTCF	chr10:97666797-97666989	Hela-S3	cervix:	n/a	n/a
4	RUNX3	chr10:97666693-97668079	GM12878	blood:	n/a	chr10:97667338-97667355
5	MAFK	chr10:97666448-97666985	HepG2	liver:	n/a	chr10:97666621-97666637 chr10:97666621-97666636
6	MTA3	chr10:97666705-97667242	GM12878	blood:	n/a	n/a
7	CTCF	chr10:97666780-97666930	HCM	heart:	n/a	n/a
8	RAD21	chr10:97666726-97667015	GM12878	blood:	n/a	n/a
9	RCOR1	chr10:97666619-97667489	GM12878	blood:	n/a	n/a
10	RCOR1	chr10:97666733-97667985	Hela-S3	cervix:	n/a	n/a
11	RAD21	chr10:97666659-97667066	HepG2	liver:	n/a	n/a
12	CTCF	chr10:97666627-97667553	K562	blood:	n/a	n/a
13	MAX	chr10:97666678-97668032	K562	blood:	n/a	chr10:97667305-97667315
14	MAFK	chr10:97666463-97668125	Hela-S3	cervix:	n/a	chr10:97666621-97666637 chr10:97666621-97666636
15	CTCF	chr10:97666797-97666978	HepG2	liver:	n/a	n/a
16	CTCF	chr10:97666705-97667709	GM12878	blood:	n/a	n/a
17	CTCF	chr10:97666760-97666910	HFF-Myc	foreskin:	n/a	n/a
18	RAD21	chr10:97666727-97667079	A549	lung:	n/a	n/a
19	CTCF	chr10:97666780-97666930	GM12878	blood:	n/a	n/a
20	MAX	chr10:97666764-97668135	SK-N-SH	brain:	n/a	chr10:97667305-97667315
21	MAFK	chr10:97666459-97666950	IMR90	lung:	n/a	chr10:97666621-97666637 chr10:97666621-97666636
22	MAFK	chr10:97666463-97666808	HepG2	liver:	n/a	chr10:97666621-97666637 chr10:97666621-97666636
23	RAD21	chr10:97666733-97667124	Hela-S3	cervix:	n/a	n/a
24	CTCF	chr10:97666778-97666975	HepG2	liver:	n/a	n/a
25	CTCF	chr10:97666760-97666910	GM12869	blood:	n/a	n/a
26	CTCF	chr10:97666780-97666930	Hela-S3	cervix:	n/a	n/a
27	MAX	chr10:97666764-97668115	Hela-S3	cervix:	n/a	chr10:97667305-97667315
28	CTCF	chr10:97666684-97667138	MCF-7	breast:	n/a	n/a
29	MYC	chr10:97666747-97668140	NB4	blood:	n/a	chr10:97667305-97667315
30	CTCF	chr10:97666780-97666930	GM12865	blood:	n/a	n/a
31	CTCF	chr10:97666760-97666910	Hela-S3	cervix:	n/a	n/a
32	MXI1	chr10:97666711-97668113	Hela-S3	cervix:	n/a	n/a
33	CTCF	chr10:97666757-97667549	IMR90	lung:	n/a	n/a
34	POLR2A	chr10:97666784-97668094	MCF10A-Er-Src	breast:	n/a	n/a
35	MYC	chr10:97666770-97668136	K562	blood:	n/a	chr10:97667305-97667315
36	RAD21	chr10:97666747-97667078	HepG2	liver:	n/a	n/a
37	CTCF	chr10:97666780-97666930	RPTEC	kidney:	n/a	n/a
38	SMC3	chr10:97666721-97667945	Hela-S3	cervix:	n/a	n/a
39	MAX	chr10:97666653-97668153	HepG2	liver:	n/a	chr10:97667305-97667315
40	CTCF	chr10:97666780-97666930	GM12864	blood:	n/a	n/a
41	RAD21	chr10:97666690-97667083	SK-N-SH_RA	brain:	n/a	n/a
42	RAD21	chr10:97666743-97667049	GM12878	blood:	n/a	n/a
43	CTCF	chr10:97666764-97667063	K562	blood:	n/a	n/a
44	SMC3	chr10:97666723-97667559	GM12878	blood:	n/a	n/a
45	CTCF	chr10:97666797-97666992	K562	blood:	n/a	n/a
46	RAD21	chr10:97666726-97667350	H1-hESC	embryonic stem cell:	n/a	n/a
47	CTCF	chr10:97666760-97666910	HA-sp	spinal cord:	n/a	n/a
48	CTCF	chr10:97666760-97666910	HCFaa	heart:	n/a	n/a
49	MAX	chr10:97666689-97668195	A549	lung:	n/a	chr10:97667305-97667315
50	TCF7L2	chr10:97666798-97668051	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:97665969..97667709-chr10:97802060..97805145,4	MCF-7	breast:

Variant related genes	Relation type
C10orf131	TF binding region
ENSG00000226688	Chromatin interaction
ENSG00000107443	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10786240	0.88[JPT][hapmap]
rs10786241	0.88[JPT][hapmap]
rs10786244	0.91[CHB][hapmap]
rs10882686	0.88[JPT][hapmap]
rs11188523	0.91[CHB][hapmap]
rs11819376	0.91[CHB][hapmap]
rs17111195	0.81[AFR][1000 genomes]
rs34078069	0.82[AFR][1000 genomes]
rs4290160	0.90[CHB][hapmap]
rs7902190	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs7905861	0.90[CHB][hapmap]
rs7922217	0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531923	chr10:97366055-97725757	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv895905	chr10:97513362-97686064	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv895906	chr10:97513362-97703650	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv895907	chr10:97529318-97686064	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv895908	chr10:97544513-97724247	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11188518	TCTN3	cis	frontal cortex	BrainEAC

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97621000-97666800	Weak transcription	Gastric	stomach
2	chr10:97628000-97666800	Weak transcription	Esophagus	oesophagus
3	chr10:97632200-97667000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr10:97634400-97666800	Weak transcription	Lung	lung
5	chr10:97634600-97666800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr10:97634800-97667000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr10:97656400-97666800	Weak transcription	Psoas Muscle	Psoas
8	chr10:97660200-97666800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr10:97660600-97666800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr10:97660600-97666800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr10:97663600-97666800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr10:97663600-97667000	Weak transcription	Spleen	Spleen
13	chr10:97663800-97666800	Weak transcription	Ovary	ovary
14	chr10:97663800-97666800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr10:97664200-97666800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr10:97664200-97666800	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr10:97664200-97666800	Weak transcription	Left Ventricle	heart
18	chr10:97664400-97666800	Weak transcription	Fetal Muscle Trunk	muscle
19	chr10:97664600-97666800	Weak transcription	Placenta	Placenta
20	chr10:97666400-97666800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr10:97666400-97666800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr10:97666400-97666800	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr10:97666400-97666800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr10:97666400-97666800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr10:97666400-97666800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr10:97666400-97666800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
27	chr10:97666400-97666800	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr10:97666400-97666800	Flanking Active TSS	Brain Anterior Caudate	brain
29	chr10:97666400-97666800	Flanking Active TSS	Fetal Brain Female	brain
30	chr10:97666400-97666800	Enhancers	Fetal Thymus	thymus
31	chr10:97666400-97666800	Flanking Active TSS	Hela-S3	cervix
32	chr10:97666400-97666800	Flanking Active TSS	HMEC	breast
33	chr10:97666400-97666800	Flanking Active TSS	HUVEC	blood vessel
34	chr10:97666400-97666800	Flanking Active TSS	NH-A	brain
35	chr10:97666400-97666800	Flanking Active TSS	NHEK	skin
36	chr10:97666400-97666800	Flanking Active TSS	NHLF	lung
37	chr10:97666400-97666800	Flanking Active TSS	Osteobl	bone
38	chr10:97666400-97667000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr10:97666400-97667000	Flanking Active TSS	Fetal Lung	lung
40	chr10:97666400-97667000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
41	chr10:97666400-97667000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr10:97666400-97667200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr10:97666400-97667200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr10:97666400-97668000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr10:97666400-97668000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr10:97666400-97668000	Active TSS	Brain Germinal Matrix	brain
47	chr10:97666400-97668000	Active TSS	Fetal Brain Male	brain
48	chr10:97666400-97668000	Active TSS	GM12878-XiMat	blood
49	chr10:97666400-97668200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr10:97666400-97668200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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