Variant report

Variant	rs12442119
Chromosome Location	chr15:83522745-83522746
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	chr15:83521559..83523474-chr15:83548872..83551411,2	MCF-7	breast:
2	chr15:83518647..83521952-chr15:83521961..83525177,3	K562	blood:

Variant related genes	Relation type
ENSG00000103942	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1256424	0.84[LWK][hapmap];0.83[MKK][hapmap]
rs12594415	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2667377	0.82[MKK][hapmap]
rs3784376	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3784377	0.94[ASW][hapmap];0.95[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4779068	1.00[YRI][hapmap]
rs899746	0.94[ASW][hapmap];0.95[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469557	chr15:83417763-83560629	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv482340	chr15:83417763-83560629	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv471687	chr15:83417764-83560629	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS 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	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12442119	ANKRD34C	cis	parietal	SCAN
rs12442119	WHAMM	cis	cerebellum	SCAN
rs12442119	BTBD1	cis	parietal	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83504600-83549400	Weak transcription	Psoas Muscle	Psoas
2	chr15:83506000-83524200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr15:83506200-83527400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:83506200-83543800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr15:83507200-83539400	Weak transcription	Fetal Intestine Small	intestine
6	chr15:83513200-83532000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr15:83514400-83542800	Weak transcription	Primary T cells from cord blood	blood
8	chr15:83516000-83523400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr15:83517800-83522800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr15:83518200-83523000	Enhancers	Fetal Thymus	thymus
11	chr15:83518400-83522800	Enhancers	Fetal Brain Male	brain
12	chr15:83518800-83524200	Weak transcription	Lung	lung
13	chr15:83519000-83523400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr15:83519000-83524200	Weak transcription	Left Ventricle	heart
15	chr15:83519000-83524400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr15:83519000-83524600	Weak transcription	Adipose Nuclei	Adipose
17	chr15:83519000-83524800	Weak transcription	Right Atrium	heart
18	chr15:83519000-83535800	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr15:83519000-83541400	Weak transcription	Brain Anterior Caudate	brain
20	chr15:83519200-83523400	Weak transcription	Colon Smooth Muscle	Colon
21	chr15:83519200-83524200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr15:83519200-83524200	Weak transcription	Right Ventricle	heart
23	chr15:83519200-83524400	Strong transcription	Gastric	stomach
24	chr15:83519200-83528800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr15:83519200-83536200	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr15:83519400-83525800	Strong transcription	Skeletal Muscle Male	skeletal muscle
27	chr15:83519600-83523400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr15:83519600-83523600	Strong transcription	Esophagus	oesophagus
29	chr15:83519600-83524200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:83519600-83524200	Weak transcription	HepG2	liver
31	chr15:83519600-83524200	Weak transcription	K562	blood
32	chr15:83519600-83525600	Weak transcription	HSMMtube	muscle
33	chr15:83519600-83529600	Weak transcription	Brain Substantia Nigra	brain
34	chr15:83519800-83523800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr15:83519800-83544400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr15:83520000-83524400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr15:83520000-83543600	Weak transcription	HSMM	muscle
38	chr15:83520000-83549800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr15:83520000-83563800	Weak transcription	Brain Hippocampus Middle	brain
40	chr15:83520200-83542000	Weak transcription	Brain Angular Gyrus	brain
41	chr15:83520200-83547000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr15:83520400-83523400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr15:83520600-83523400	Strong transcription	Stomach Smooth Muscle	stomach
44	chr15:83520600-83523600	Strong transcription	Fetal Stomach	stomach
45	chr15:83520800-83522800	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr15:83521000-83524200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr15:83521000-83524400	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr15:83521200-83522800	Enhancers	Thymus	Thymus
49	chr15:83521600-83524600	Weak transcription	Osteobl	bone
50	chr15:83521800-83523600	Genic enhancers	Pancreas	Pancrea

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