Variant report

Variant	rs11164043
Chromosome Location	chr1:85167337-85167338
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	chr1:85155313..85157722-chr1:85164509..85167486,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117155	Chromatin interaction

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]
rs11164044	0.90[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	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11802347	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12024245	0.91[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];0.91[YRI][hapmap];0.86[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	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1340529	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1578329	0.95[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	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6576721	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	0.87[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.88[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	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72952199	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72954003	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72954029	0.92[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	0.94[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]
rs7553039	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs11164043	COL24A1	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85163000-85168400	Enhancers	Rectal Smooth Muscle	rectum
2	chr1:85163600-85168400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:85164200-85167800	Enhancers	Primary T cells from cord blood	blood
4	chr1:85164400-85167800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:85164800-85167400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr1:85164800-85167400	Enhancers	NHLF	lung
7	chr1:85164800-85168000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr1:85164800-85169600	Weak transcription	Fetal Lung	lung
9	chr1:85164800-85170200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr1:85164800-85170800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:85164800-85170800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr1:85164800-85171000	Weak transcription	Fetal Kidney	kidney
13	chr1:85165000-85169600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr1:85165200-85170200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr1:85165200-85179000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:85165800-85167400	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr1:85166000-85168400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:85166000-85168400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:85166200-85167400	Weak transcription	Fetal Brain Male	brain
20	chr1:85166200-85168400	Weak transcription	Fetal Muscle Leg	muscle
21	chr1:85166200-85169600	Weak transcription	Fetal Intestine Large	intestine
22	chr1:85166200-85170200	Weak transcription	Primary B cells from peripheral blood	blood
23	chr1:85166200-85170600	Weak transcription	K562	blood
24	chr1:85166200-85173400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:85166400-85168200	Weak transcription	Colon Smooth Muscle	Colon
26	chr1:85166400-85169600	Weak transcription	Fetal Intestine Small	intestine
27	chr1:85166400-85170200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr1:85166400-85170400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:85167000-85167400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:85167200-85167400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:85167200-85167400	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr1:85167200-85167400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:85167200-85167400	Enhancers	Primary B cells from cord blood	blood
34	chr1:85167200-85167400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
35	chr1:85167200-85167400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:85167200-85167400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
37	chr1:85167200-85167400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:85167200-85167400	Flanking Active TSS	HSMM	muscle
39	chr1:85167200-85167400	Flanking Active TSS	Osteobl	bone
40	chr1:85167200-85167600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:85167200-85167600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:85167200-85167600	Active TSS	Aorta	Aorta
43	chr1:85167200-85167600	Active TSS	Fetal Brain Female	brain
44	chr1:85167200-85167600	Active TSS	Fetal Muscle Trunk	muscle
45	chr1:85167200-85167600	Active TSS	Psoas Muscle	Psoas
46	chr1:85167200-85167600	Active TSS	Right Atrium	heart
47	chr1:85167200-85167600	Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr1:85167200-85167600	Active TSS	Stomach Smooth Muscle	stomach
49	chr1:85167200-85167600	Active TSS	HSMMtube	muscle
50	chr1:85167200-85168000	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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