Variant report

Variant	rs4898844
Chromosome Location	chr14:55122827-55122828
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:55122538..55124044-chr14:55126253..55128452,2	MCF-7	breast:
2	chr14:55121459..55123514-chr14:55126031..55127873,3	MCF-7	breast:
3	chr14:55112933..55122073-chr14:55122136..55129636,16	MCF-7	breast:
4	chr14:55119482..55121341-chr14:55121641..55124299,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000020577	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11158019	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12586228	0.88[EUR][1000 genomes]
rs12586646	0.92[ASN][1000 genomes]
rs12586705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12590927	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12888372	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12890352	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17728293	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2025130	0.85[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs35399674	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4553503	0.94[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs7151563	0.83[ASN][1000 genomes]
rs7155089	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7158091	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.92[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8011374	0.89[CEU][hapmap];0.93[GIH][hapmap];0.80[MEX][hapmap];0.82[YRI][hapmap]
rs8022597	0.85[ASN][1000 genomes]
rs911621	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[ASN][1000 genomes]
rs942607	0.84[CEU][hapmap];0.91[TSI][hapmap];0.88[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4898844	RSPH4A	trans	parietal	SCAN
rs4898844	PTGER2	cis	cerebellum	SCAN
rs4898844	OR5AR1	trans	parietal	SCAN
rs4898844	GNPNAT1	cis	parietal	SCAN
rs4898844	C14orf178	trans	cerebellum	SCAN
rs4898844	BMP4	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55117600-55129400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr14:55119000-55132400	Enhancers	HepG2	liver
3	chr14:55119800-55135800	Weak transcription	Fetal Brain Male	brain
4	chr14:55120000-55179400	Weak transcription	Fetal Intestine Small	intestine
5	chr14:55120200-55124600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr14:55120800-55125600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr14:55120800-55137400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr14:55121000-55123200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr14:55121000-55124600	Weak transcription	NHEK	skin
10	chr14:55121000-55138200	Weak transcription	Aorta	Aorta
11	chr14:55121200-55124400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr14:55121200-55126800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr14:55121400-55136400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr14:55121600-55124000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr14:55121600-55125200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr14:55121600-55125200	Weak transcription	Colon Smooth Muscle	Colon
17	chr14:55121600-55125400	Weak transcription	Placenta	Placenta
18	chr14:55121600-55127200	Weak transcription	Brain Anterior Caudate	brain
19	chr14:55121600-55129400	Weak transcription	Fetal Stomach	stomach
20	chr14:55121600-55129600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr14:55121800-55124400	Weak transcription	HMEC	breast
22	chr14:55121800-55125200	Weak transcription	Lung	lung
23	chr14:55121800-55125200	Weak transcription	Psoas Muscle	Psoas
24	chr14:55121800-55125400	Weak transcription	A549	lung
25	chr14:55121800-55128400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr14:55121800-55135600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr14:55121800-55135800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr14:55121800-55135800	Weak transcription	NH-A	brain
29	chr14:55122000-55123800	Weak transcription	Fetal Heart	heart
30	chr14:55122000-55124200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr14:55122000-55124200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr14:55122000-55124400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr14:55122000-55124800	Weak transcription	Fetal Muscle Leg	muscle
34	chr14:55122000-55125200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr14:55122000-55125200	Weak transcription	Spleen	Spleen
36	chr14:55122000-55125400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr14:55122000-55126400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr14:55122000-55126600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr14:55122000-55127200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr14:55122000-55127200	Weak transcription	HSMMtube	muscle
41	chr14:55122000-55131000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr14:55122000-55134000	Weak transcription	Brain Substantia Nigra	brain
43	chr14:55122000-55134200	Weak transcription	NHLF	lung
44	chr14:55122000-55136200	Weak transcription	Osteobl	bone
45	chr14:55122200-55124400	Weak transcription	Left Ventricle	heart
46	chr14:55122200-55124400	Weak transcription	HUVEC	blood vessel
47	chr14:55122200-55125000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr14:55122200-55125200	Weak transcription	Right Atrium	heart
49	chr14:55122200-55125200	Weak transcription	Right Ventricle	heart
50	chr14:55122200-55125400	Weak transcription	Adipose Nuclei	Adipose

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