Variant report

Variant	rs7553039
Chromosome Location	chr1:85168511-85168512
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	chr1:85153044..85155913-chr1:85168206..85170903,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11164027	0.85[CEU][hapmap]
rs11164029	0.81[EUR][1000 genomes]
rs11164030	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs11164043	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164044	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11164046	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11802347	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12024245	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12025014	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12031476	0.92[CEU][hapmap];0.84[GIH][hapmap]
rs12042947	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12045905	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12409045	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1340529	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1578329	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17113051	0.85[CEU][hapmap];0.87[GIH][hapmap]
rs17113057	0.84[GIH][hapmap]
rs17114425	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2911568	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs2911613	0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs4506477	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6576721	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6659803	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6686971	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6695249	0.85[CEU][hapmap];0.84[GIH][hapmap]
rs72952191	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72952199	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72954003	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72954029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7512978	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7529024	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7530459	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7536572	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs818521	0.81[CHB][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.84[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7553039	COL24A1	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85164800-85169600	Weak transcription	Fetal Lung	lung
2	chr1:85164800-85170200	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr1:85164800-85170800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:85164800-85170800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:85164800-85171000	Weak transcription	Fetal Kidney	kidney
6	chr1:85165000-85169600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr1:85165200-85170200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:85165200-85179000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:85166200-85169600	Weak transcription	Fetal Intestine Large	intestine
10	chr1:85166200-85170200	Weak transcription	Primary B cells from peripheral blood	blood
11	chr1:85166200-85170600	Weak transcription	K562	blood
12	chr1:85166200-85173400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:85166400-85169600	Weak transcription	Fetal Intestine Small	intestine
14	chr1:85166400-85170200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr1:85166400-85170400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:85167200-85168600	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr1:85167200-85168600	Enhancers	Fetal Stomach	stomach
18	chr1:85167200-85168800	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr1:85167400-85168800	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr1:85167400-85168800	Enhancers	Fetal Brain Male	brain
21	chr1:85167400-85169600	Weak transcription	Primary B cells from cord blood	blood
22	chr1:85167600-85168800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:85167600-85169800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:85167600-85171400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:85167600-85173800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr1:85167600-85177000	Weak transcription	Aorta	Aorta
27	chr1:85167800-85168600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:85167800-85168800	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr1:85167800-85170000	Enhancers	Fetal Brain Female	brain
30	chr1:85168000-85168600	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr1:85168200-85168600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:85168200-85168600	Enhancers	Colon Smooth Muscle	Colon
33	chr1:85168200-85169400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:85168400-85168600	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr1:85168400-85168600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr1:85168400-85168600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr1:85168400-85168600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:85168400-85168600	Enhancers	Fetal Muscle Leg	muscle
39	chr1:85168400-85168600	Enhancers	Placenta	Placenta
40	chr1:85168400-85168600	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr1:85168400-85176800	Weak transcription	Rectal Smooth Muscle	rectum

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