Variant report

Variant	rs34047494
Chromosome Location	chr12:123934070-123934071
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123933826..123935553-chr12:123942012..123946066,3	K562	blood:
2	chr12:123933826..123935553-chr12:123942012..123944583,2	K562	blood:
3	chr12:123933115..123935962-chr12:123941245..123944005,2	MCF-7	breast:
4	chr12:123933162..123935586-chr12:123941113..123943994,3	MCF-7	breast:
5	chr12:123918432..123921016-chr12:123934034..123936294,2	K562	blood:

Variant related genes	Relation type
ENSG00000184209	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11507739	0.94[EUR][1000 genomes]
rs11507740	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13303080	0.83[EUR][1000 genomes]
rs13303107	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13303167	0.87[EUR][1000 genomes]
rs13303200	0.95[CEU][hapmap];0.91[MEX][hapmap];0.83[EUR][1000 genomes]
rs13303266	0.91[EUR][1000 genomes]
rs13303334	0.85[TSI][hapmap]
rs28413969	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28483351	0.93[EUR][1000 genomes]
rs28497891	0.83[EUR][1000 genomes]
rs28557411	0.82[EUR][1000 genomes]
rs28667043	0.90[EUR][1000 genomes]
rs28691687	1.00[CHD][hapmap]
rs34351395	0.95[CEU][hapmap];0.91[MEX][hapmap];0.83[EUR][1000 genomes]
rs34762274	0.83[EUR][1000 genomes]
rs35090528	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35157218	0.87[EUR][1000 genomes]
rs35370271	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35970945	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]
rs36084544	0.83[EUR][1000 genomes]
rs4047517	0.91[EUR][1000 genomes]
rs56412477	0.89[EUR][1000 genomes]
rs56860279	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6606748	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71456799	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7297035	0.88[EUR][1000 genomes]
rs7300562	0.89[EUR][1000 genomes]
rs7306670	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7315901	0.89[EUR][1000 genomes]
rs7960816	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7975122	0.93[EUR][1000 genomes]
rs7978323	0.89[EUR][1000 genomes]
rs9330649	0.80[EUR][1000 genomes]
rs9330650	0.92[TSI][hapmap]
rs9697459	0.82[EUR][1000 genomes]
rs9697581	0.83[EUR][1000 genomes]
rs9697628	0.85[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs9697735	0.85[CEU][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs9778001	0.83[EUR][1000 genomes]
rs9803116	0.86[AMR][1000 genomes];0.86[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs34047494	TCTN2	cis	parietal	SCAN
rs34047494	MLXIP	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123930800-123935600	Weak transcription	Fetal Intestine Small	intestine
2	chr12:123932600-123934200	Enhancers	Placenta	Placenta
3	chr12:123933000-123934800	Enhancers	Hela-S3	cervix
4	chr12:123933200-123934400	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr12:123933400-123934200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr12:123933400-123934200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr12:123933400-123934200	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr12:123933400-123934200	Enhancers	GM12878-XiMat	blood
9	chr12:123933400-123934400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr12:123933400-123934400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr12:123933400-123934600	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr12:123933400-123935200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr12:123933400-123942200	Weak transcription	Thymus	Thymus
14	chr12:123933600-123934200	Enhancers	Primary T cells fromperipheralblood	blood
15	chr12:123933600-123934200	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr12:123933600-123934200	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr12:123933600-123934200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr12:123933600-123934200	Flanking Active TSS	HepG2	liver
19	chr12:123933600-123934400	Enhancers	Primary hematopoietic stem cells	blood
20	chr12:123933600-123934400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr12:123933800-123934200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr12:123933800-123934200	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr12:123933800-123934200	Enhancers	NHDF-Ad	bronchial
24	chr12:123933800-123934200	Enhancers	Osteobl	bone
25	chr12:123933800-123934400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:123933800-123934400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr12:123933800-123934800	Enhancers	K562	blood
28	chr12:123934000-123934200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr12:123934000-123934200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr12:123934000-123934200	Enhancers	Spleen	Spleen
31	chr12:123934000-123934600	Enhancers	Primary neutrophils fromperipheralblood	blood

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