Variant report

Variant	rs16858949
Chromosome Location	chr3:111683120-111683121
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:111664159..111666213-chr3:111682132..111684444,2	MCF-7	breast:
2	chr3:111681073..111684154-chr3:111684668..111686720,3	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11917711	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11928983	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11928985	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1283003	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13062225	0.86[MEX][hapmap]
rs16858950	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16858964	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs522573	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6785350	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6788215	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6788410	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6800933	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73230499	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73232014	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73232025	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774856	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774857	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774860	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774861	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774862	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16858949	WDYHV1	trans	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111637200-111690600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:111642200-111690400	Weak transcription	Spleen	Spleen
3	chr3:111645400-111689600	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr3:111652400-111685800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr3:111653000-111686200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:111654400-111695000	Strong transcription	Placenta	Placenta
7	chr3:111658600-111697400	Weak transcription	Gastric	stomach
8	chr3:111658800-111685800	Weak transcription	HepG2	liver
9	chr3:111661600-111689800	Weak transcription	Ovary	ovary
10	chr3:111666600-111697400	Weak transcription	Esophagus	oesophagus
11	chr3:111670800-111685000	Strong transcription	Liver	Liver
12	chr3:111672800-111686000	Weak transcription	Fetal Intestine Small	intestine
13	chr3:111673000-111688400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:111673000-111688400	Weak transcription	Fetal Stomach	stomach
15	chr3:111673000-111697400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:111673000-111697400	Weak transcription	Pancreas	Pancrea
17	chr3:111673600-111686000	Weak transcription	Fetal Kidney	kidney
18	chr3:111675000-111697400	Weak transcription	Lung	lung
19	chr3:111675800-111685200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:111676800-111685800	Weak transcription	Fetal Lung	lung
21	chr3:111678200-111683400	Strong transcription	Left Ventricle	heart
22	chr3:111678200-111687800	Weak transcription	Right Ventricle	heart
23	chr3:111678200-111692800	Weak transcription	Aorta	Aorta
24	chr3:111678400-111685600	Strong transcription	Adipose Nuclei	Adipose
25	chr3:111680200-111683200	Enhancers	NHDF-Ad	bronchial
26	chr3:111680400-111683600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:111680600-111683600	Strong transcription	Fetal Intestine Large	intestine
28	chr3:111680600-111684200	Strong transcription	Fetal Muscle Leg	muscle
29	chr3:111680600-111686400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:111680800-111683200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr3:111681000-111683600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:111681000-111685800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr3:111681000-111686000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr3:111681000-111686000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr3:111681200-111683200	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr3:111681200-111686000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr3:111681200-111686400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:111681200-111686400	Weak transcription	Fetal Thymus	thymus
39	chr3:111681200-111689800	Weak transcription	Thymus	Thymus
40	chr3:111681400-111683800	Weak transcription	Fetal Heart	heart
41	chr3:111681400-111685600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:111681400-111687000	Weak transcription	Stomach Smooth Muscle	stomach
43	chr3:111681400-111694400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:111681400-111697200	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr3:111681400-111697400	Weak transcription	Rectal Smooth Muscle	rectum
46	chr3:111681800-111683200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:111682000-111683200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr3:111682200-111687000	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr3:111682400-111689800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:111682400-111694600	Strong transcription	NH-A	brain

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