Variant report

Variant	rs35970945
Chromosome Location	chr12:123955358-123955359
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123954067..123957606-chr12:124016638..124019089,3	MCF-7	breast:
2	chr12:123950525..123953313-chr12:123954953..123957531,2	MCF-7	breast:
3	chr12:123848006..123850199-chr12:123954531..123957237,2	MCF-7	breast:
4	chr12:123941355..123944162-chr12:123954401..123956656,2	K562	blood:
5	chr12:123948778..123953416-chr12:123953598..123956451,4	K562	blood:

Variant related genes	Relation type
ENSG00000184209	Chromatin interaction
ENSG00000139697	Chromatin interaction
ENSG00000256092	Chromatin interaction
ENSG00000188026	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11507739	0.87[EUR][1000 genomes]
rs11507740	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13303080	0.89[EUR][1000 genomes]
rs13303107	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13303167	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13303200	0.95[CEU][hapmap];0.82[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes]
rs13303266	0.91[EUR][1000 genomes]
rs13303334	0.85[TSI][hapmap]
rs28413969	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28483351	0.86[EUR][1000 genomes]
rs28497891	0.87[EUR][1000 genomes]
rs28557411	0.87[EUR][1000 genomes]
rs28667043	0.94[EUR][1000 genomes]
rs34047494	1.00[CEU][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34351395	0.95[CEU][hapmap];0.82[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes]
rs34762274	0.89[EUR][1000 genomes]
rs35090528	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35157218	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35370271	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36084544	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4047517	0.91[EUR][1000 genomes]
rs56412477	1.00[EUR][1000 genomes]
rs56860279	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6606748	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71456799	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7297035	0.91[EUR][1000 genomes]
rs7300562	0.93[EUR][1000 genomes]
rs7306670	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7315901	0.92[EUR][1000 genomes]
rs7960816	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7975122	0.93[EUR][1000 genomes]
rs7978323	0.92[EUR][1000 genomes]
rs9330649	0.84[EUR][1000 genomes]
rs9330650	0.92[TSI][hapmap]
rs9697459	0.87[EUR][1000 genomes]
rs9697581	0.89[EUR][1000 genomes]
rs9697628	0.85[CEU][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs9697735	0.85[CEU][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs9777736	0.80[EUR][1000 genomes]
rs9778001	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9803116	0.96[AMR][1000 genomes];0.98[EUR][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35970945	TCTN2	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123943600-123955800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:123943800-123956000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:123943800-123956400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr12:123943800-123958800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:123943800-123959600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:123943800-123959600	Weak transcription	Psoas Muscle	Psoas
7	chr12:123943800-123961200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr12:123944400-123955800	Weak transcription	NHEK	skin
9	chr12:123944600-123956400	Weak transcription	Stomach Mucosa	stomach
10	chr12:123944600-123995600	Weak transcription	Hela-S3	cervix
11	chr12:123944600-124012200	Strong transcription	Fetal Stomach	stomach
12	chr12:123944800-123964600	Weak transcription	Small Intestine	intestine
13	chr12:123945200-123959200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr12:123945800-123965600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:123946000-123965600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:123946200-123957600	Strong transcription	Fetal Thymus	thymus
17	chr12:123946200-123957800	Strong transcription	Fetal Muscle Leg	muscle
18	chr12:123946800-123959200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr12:123947200-123958600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr12:123947600-123971800	Strong transcription	Fetal Intestine Small	intestine
21	chr12:123947800-123955800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:123948200-123962800	Strong transcription	Fetal Muscle Trunk	muscle
23	chr12:123949000-123957800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:123949000-123966200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:123949000-123984400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr12:123949200-123955800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:123949200-123957600	Strong transcription	Primary T cells from cord blood	blood
28	chr12:123949200-123957600	Strong transcription	Stomach Smooth Muscle	stomach
29	chr12:123949600-123956200	Weak transcription	NH-A	brain
30	chr12:123950000-123963200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr12:123950400-123955800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr12:123950400-123955800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr12:123950400-123956000	Weak transcription	Fetal Kidney	kidney
34	chr12:123950400-123956000	Weak transcription	NHDF-Ad	bronchial
35	chr12:123950400-123973000	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr12:123950600-123955800	Weak transcription	Aorta	Aorta
37	chr12:123950600-123956000	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr12:123950600-123956000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr12:123950600-123958800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr12:123950600-123958800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr12:123950800-123955800	Weak transcription	Esophagus	oesophagus
42	chr12:123950800-123955800	Weak transcription	Left Ventricle	heart
43	chr12:123950800-123955800	Weak transcription	Ovary	ovary
44	chr12:123950800-123955800	Weak transcription	Right Ventricle	heart
45	chr12:123950800-123956000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr12:123950800-123956000	Weak transcription	Pancreas	Pancrea
47	chr12:123950800-123956000	Weak transcription	HMEC	breast
48	chr12:123950800-123956200	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr12:123950800-123956200	Weak transcription	K562	blood
50	chr12:123950800-123956400	Weak transcription	Fetal Brain Male	brain

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