Variant report

Variant	rs942607
Chromosome Location	chr14:55111102-55111103
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:55031933..55036360-chr14:55108967..55113737,8	MCF-7	breast:
2	chr14:55110011..55112395-chr14:55239108..55242074,2	K562	blood:

Variant related genes	Relation type
ENSG00000020577	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11158019	0.92[EUR][1000 genomes]
rs12586228	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12586705	0.94[EUR][1000 genomes]
rs12590927	0.88[EUR][1000 genomes]
rs12888372	0.81[CEU][hapmap];0.94[EUR][1000 genomes]
rs12890352	0.84[CEU][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs17728293	0.91[ASW][hapmap];0.84[CEU][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs35399674	0.94[EUR][1000 genomes]
rs4898844	0.84[CEU][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs7158091	0.91[ASW][hapmap];0.84[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv974464	chr14:55092217-55152792	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs942607	BMP4	cis	parietal	SCAN
rs942607	PTGER2	cis	cerebellum	SCAN
rs942607	RSPH4A	trans	parietal	SCAN
rs942607	C14orf178	trans	cerebellum	SCAN
rs942607	GNPNAT1	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55070400-55116200	Weak transcription	HMEC	breast
2	chr14:55103600-55116600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr14:55105200-55116000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr14:55105400-55116000	Weak transcription	NHEK	skin
5	chr14:55105600-55111600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr14:55105800-55113000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr14:55106000-55111400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr14:55106400-55116000	Weak transcription	HSMM	muscle
9	chr14:55106400-55117800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr14:55106600-55113600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr14:55107400-55117200	Weak transcription	Fetal Stomach	stomach
12	chr14:55107600-55112400	Weak transcription	Adipose Nuclei	Adipose
13	chr14:55107600-55117000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr14:55107600-55118000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr14:55107600-55121400	Weak transcription	Pancreas	Pancrea
16	chr14:55107800-55112400	Weak transcription	NHDF-Ad	bronchial
17	chr14:55107800-55116600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr14:55108000-55112600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr14:55108200-55114200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr14:55108600-55111600	Enhancers	Fetal Heart	heart
21	chr14:55108800-55111400	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr14:55109000-55111600	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr14:55109000-55111600	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr14:55109200-55111400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr14:55109200-55111400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr14:55109200-55111400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr14:55109200-55111400	Enhancers	NHLF	lung
28	chr14:55109200-55111600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr14:55109200-55113400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr14:55109400-55111200	Enhancers	Placenta Amnion	Placenta Amnion
31	chr14:55109400-55111400	Enhancers	Aorta	Aorta
32	chr14:55109400-55111400	Enhancers	Placenta	Placenta
33	chr14:55109400-55111400	Enhancers	Right Atrium	heart
34	chr14:55109400-55111400	Enhancers	NH-A	brain
35	chr14:55109600-55121400	Weak transcription	Spleen	Spleen
36	chr14:55109800-55113000	Weak transcription	Gastric	stomach
37	chr14:55109800-55114600	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr14:55109800-55115000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr14:55109800-55115400	Weak transcription	Brain Anterior Caudate	brain
40	chr14:55109800-55116600	Weak transcription	Brain Hippocampus Middle	brain
41	chr14:55109800-55117200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr14:55109800-55119400	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr14:55110000-55113000	Weak transcription	Right Ventricle	heart
44	chr14:55110200-55114600	Weak transcription	Brain Substantia Nigra	brain
45	chr14:55110200-55116200	Weak transcription	A549	lung
46	chr14:55110200-55117000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr14:55110400-55114000	Weak transcription	HUVEC	blood vessel
48	chr14:55110400-55114600	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr14:55110400-55116000	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr14:55110400-55116200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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