Variant report

Variant	rs13303200
Chromosome Location	chr12:123981144-123981145
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123981034..123983200-chr12:124016906..124019887,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188026	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11507739	0.82[EUR][1000 genomes]
rs11507740	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13303044	0.85[EUR][1000 genomes]
rs13303080	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13303107	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13303167	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13303189	0.81[EUR][1000 genomes]
rs13303217	0.82[EUR][1000 genomes]
rs13303266	0.85[EUR][1000 genomes]
rs13303334	0.88[GIH][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs28413969	0.89[EUR][1000 genomes]
rs28483351	0.80[EUR][1000 genomes]
rs28497891	0.94[EUR][1000 genomes]
rs28557411	0.94[EUR][1000 genomes]
rs28667043	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34047494	0.95[CEU][hapmap];0.91[MEX][hapmap];0.83[EUR][1000 genomes]
rs34351395	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34762274	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35090528	0.90[EUR][1000 genomes]
rs35157218	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35370271	0.90[EUR][1000 genomes]
rs35970945	0.95[CEU][hapmap];0.82[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes]
rs36084544	0.90[EUR][1000 genomes]
rs4047517	0.85[EUR][1000 genomes]
rs56412477	0.89[EUR][1000 genomes]
rs56860279	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6606748	0.91[EUR][1000 genomes]
rs71456799	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7297035	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7300562	0.87[EUR][1000 genomes]
rs7306670	0.88[EUR][1000 genomes]
rs7315901	0.86[EUR][1000 genomes]
rs7960816	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7975122	0.88[EUR][1000 genomes]
rs7978323	0.86[EUR][1000 genomes]
rs9330649	0.96[EUR][1000 genomes]
rs9330650	0.84[CEU][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs9697459	0.94[EUR][1000 genomes]
rs9697581	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9697628	0.90[CEU][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes]
rs9697735	0.90[CEU][hapmap];0.87[TSI][hapmap];0.94[EUR][1000 genomes]
rs9777736	0.87[EUR][1000 genomes]
rs9778001	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9803116	0.89[EUR][1000 genomes]

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	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1035223	chr12:123795559-123991706	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS 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	48 gene(s)	inside rSNPs	diseases
4	esv1822004	chr12:123919287-124013451	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1037260	chr12:123956749-124023069	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13303200	TCTN2	cis	parietal	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123944600-123995600	Weak transcription	Hela-S3	cervix
2	chr12:123944600-124012200	Strong transcription	Fetal Stomach	stomach
3	chr12:123949000-123984400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr12:123950800-124007600	Weak transcription	Colonic Mucosa	Colon
5	chr12:123956800-123993400	Weak transcription	HMEC	breast
6	chr12:123956800-123995400	Weak transcription	Fetal Brain Male	brain
7	chr12:123957400-123982400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr12:123957400-123995400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr12:123957400-123995400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr12:123957600-123995400	Weak transcription	Pancreas	Pancrea
11	chr12:123957600-124003800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr12:123957800-123982600	Weak transcription	A549	lung
13	chr12:123960000-123995400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:123961600-123995800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr12:123963000-123981200	Weak transcription	Esophagus	oesophagus
16	chr12:123964200-123981200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:123964200-123981200	Weak transcription	Spleen	Spleen
18	chr12:123964200-123981400	Weak transcription	NHDF-Ad	bronchial
19	chr12:123964400-123981200	Weak transcription	Gastric	stomach
20	chr12:123965400-123981400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr12:123965400-123983000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr12:123965600-123981200	Weak transcription	NHLF	lung
23	chr12:123965600-123982600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr12:123968800-123981200	Weak transcription	Liver	Liver
25	chr12:123968800-123995400	Weak transcription	NH-A	brain
26	chr12:123969000-123993800	Weak transcription	HUVEC	blood vessel
27	chr12:123969400-123984600	Weak transcription	Thymus	Thymus
28	chr12:123969800-123982600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr12:123970000-124016400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr12:123973600-123995400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr12:123973800-123982400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr12:123974600-123995400	Weak transcription	Dnd41	blood
33	chr12:123974800-123982200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr12:123975200-123981200	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr12:123975600-123985400	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr12:123977400-123994200	Weak transcription	Fetal Heart	heart
37	chr12:123977600-123982200	Weak transcription	HSMMtube	muscle
38	chr12:123978400-123984200	Strong transcription	Stomach Smooth Muscle	stomach
39	chr12:123978400-123985800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr12:123978600-123981200	Weak transcription	Placenta	Placenta
41	chr12:123978600-123982000	Strong transcription	Brain Germinal Matrix	brain
42	chr12:123978800-123982400	Weak transcription	HepG2	liver
43	chr12:123978800-123984000	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr12:123978800-123984800	Strong transcription	Fetal Intestine Small	intestine
45	chr12:123979000-123984000	Strong transcription	Adipose Nuclei	Adipose
46	chr12:123979000-123984400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr12:123979200-123983000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:123979200-123984600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr12:123979400-123981200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr12:123979400-123981200	Weak transcription	Psoas Muscle	Psoas

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