Variant report

Variant	rs4683550
Chromosome Location	chr3:140804298-140804299
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	chr3:140802398..140804729-chr3:140810724..140812835,2	MCF-7	breast:
2	chr3:140798316..140800500-chr3:140804270..140806096,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11919846	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11919859	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11925565	1.00[EUR][1000 genomes]
rs11927097	0.82[EUR][1000 genomes]
rs11928846	0.81[CEU][hapmap]
rs1365631	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2086180	0.90[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs35816243	0.82[EUR][1000 genomes]
rs4683391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683392	0.99[EUR][1000 genomes]
rs4683393	0.99[EUR][1000 genomes]
rs4683394	0.82[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs4683546	0.90[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap]
rs4683547	0.90[CEU][hapmap];0.97[EUR][1000 genomes]
rs4683548	0.97[EUR][1000 genomes]
rs4683549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683552	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683558	0.86[EUR][1000 genomes]
rs59179278	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59276022	0.90[EUR][1000 genomes]
rs59870469	0.81[EUR][1000 genomes]
rs62283579	0.96[EUR][1000 genomes]
rs62283580	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62283582	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62283585	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62283586	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62283587	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62283588	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62283592	0.88[EUR][1000 genomes]
rs62283593	0.88[EUR][1000 genomes]
rs62283596	0.86[EUR][1000 genomes]
rs62283597	0.88[EUR][1000 genomes]
rs62283598	0.88[EUR][1000 genomes]
rs62283600	0.88[EUR][1000 genomes]
rs62283603	0.82[EUR][1000 genomes]
rs62283605	0.81[EUR][1000 genomes]
rs6650888	0.88[EUR][1000 genomes]
rs72980182	0.97[EUR][1000 genomes]
rs72980194	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72981978	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72981996	0.90[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4683550	CHST2	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140792800-140808400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr3:140793400-140806600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:140794000-140813000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:140796600-140806600	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr3:140796600-140807200	Enhancers	Fetal Heart	heart
6	chr3:140797000-140804400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:140797000-140805000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr3:140797200-140811200	Weak transcription	Fetal Brain Male	brain
9	chr3:140797800-140804600	Weak transcription	Fetal Brain Female	brain
10	chr3:140798400-140804600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:140798400-140806800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:140799600-140805200	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr3:140799600-140808600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:140801200-140807200	Enhancers	Fetal Muscle Leg	muscle
15	chr3:140802000-140806600	Enhancers	Brain Germinal Matrix	brain
16	chr3:140802000-140807400	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr3:140802200-140805000	Enhancers	HSMM	muscle
18	chr3:140802200-140806400	Enhancers	Psoas Muscle	Psoas
19	chr3:140802400-140804800	Enhancers	Fetal Muscle Trunk	muscle
20	chr3:140802400-140804800	Enhancers	Right Ventricle	heart
21	chr3:140802600-140805600	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr3:140802600-140805800	Enhancers	Adipose Nuclei	Adipose
23	chr3:140802800-140804600	Strong transcription	Dnd41	blood
24	chr3:140802800-140804800	Enhancers	Fetal Kidney	kidney
25	chr3:140803000-140804400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr3:140803000-140804600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr3:140803000-140813800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr3:140803200-140804600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr3:140803200-140808400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr3:140803400-140805200	Weak transcription	Right Atrium	heart
31	chr3:140803400-140810000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr3:140803600-140804400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
33	chr3:140803600-140805000	Enhancers	H9 Cell Line	embryonic stem cell
34	chr3:140803800-140804800	Weak transcription	Fetal Stomach	stomach
35	chr3:140803800-140806000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:140803800-140806400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:140803800-140806600	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr3:140803800-140807000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr3:140803800-140808000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:140804000-140804400	Weak transcription	Colon Smooth Muscle	Colon
41	chr3:140804000-140804600	Weak transcription	Placenta	Placenta
42	chr3:140804000-140804800	Enhancers	Pancreas	Pancrea
43	chr3:140804000-140805200	Weak transcription	Fetal Lung	lung
44	chr3:140804000-140806000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr3:140804200-140804600	Weak transcription	HSMMtube	muscle
46	chr3:140804200-140805800	Weak transcription	Left Ventricle	heart
47	chr3:140804200-140806400	Enhancers	Stomach Smooth Muscle	stomach
48	chr3:140804200-140807200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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