Variant report

Variant	rs6686971
Chromosome Location	chr1:85152809-85152810
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:85148980..85153472-chr1:85154785..85157267,4	MCF-7	breast:
2	chr1:85151664..85154712-chr1:85171325..85174497,4	K562	blood:
3	chr1:85152648..85155097-chr1:85155098..85157489,2	MCF-7	breast:
4	chr1:85150908..85155231-chr1:85184814..85188587,5	K562	blood:

Variant related genes	Relation type
ENSG00000117155	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11164027	0.93[CEU][hapmap]
rs11164029	0.84[EUR][1000 genomes]
rs11164030	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs11164043	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]
rs11164044	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11164046	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164047	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11802347	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12024245	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12025014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12031476	1.00[CEU][hapmap];0.84[GIH][hapmap];0.83[MEX][hapmap]
rs12042947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12045905	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12409045	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1340529	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1578329	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17113051	0.93[CEU][hapmap];0.87[GIH][hapmap];0.89[MEX][hapmap];0.83[EUR][1000 genomes]
rs17113057	0.81[CEU][hapmap];0.84[GIH][hapmap];0.89[MEX][hapmap]
rs17114425	0.86[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	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6576721	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6659803	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6695249	0.93[CEU][hapmap];0.84[GIH][hapmap];0.83[MEX][hapmap]
rs72952191	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72952199	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72954003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72954029	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7512978	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7529024	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7530459	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7536572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7553039	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs818521	0.81[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][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	nsv947283	chr1:85150944-85155058	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6686971	COL24A1	cis	parietal	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85106400-85155400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:85108000-85155000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:85124600-85154400	Weak transcription	A549	lung
4	chr1:85124800-85153800	Weak transcription	Hela-S3	cervix
5	chr1:85125000-85153400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:85125000-85153600	Weak transcription	Fetal Kidney	kidney
7	chr1:85126200-85154000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr1:85126400-85154200	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr1:85126400-85154800	Weak transcription	Fetal Muscle Leg	muscle
10	chr1:85126400-85155200	Weak transcription	Left Ventricle	heart
11	chr1:85126600-85153400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr1:85126600-85154400	Weak transcription	Fetal Stomach	stomach
13	chr1:85127800-85154400	Weak transcription	Brain Germinal Matrix	brain
14	chr1:85128200-85153600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:85128600-85153200	Weak transcription	Dnd41	blood
16	chr1:85130400-85153600	Weak transcription	NHDF-Ad	bronchial
17	chr1:85134400-85153400	Weak transcription	NHLF	lung
18	chr1:85138000-85154800	Weak transcription	HSMMtube	muscle
19	chr1:85138400-85153400	Weak transcription	Fetal Thymus	thymus
20	chr1:85138600-85153400	Weak transcription	HSMM	muscle
21	chr1:85138800-85155000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:85139800-85153000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr1:85140000-85154200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr1:85140800-85153400	Weak transcription	NHEK	skin
25	chr1:85141000-85153600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:85141000-85154200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:85141000-85154200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr1:85141400-85154200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:85141800-85154200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr1:85142200-85154200	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr1:85142200-85154200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:85143600-85153400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:85143600-85154600	Weak transcription	Primary B cells from cord blood	blood
34	chr1:85143800-85154200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr1:85144400-85154400	Weak transcription	Primary hematopoietic stem cells	blood
36	chr1:85144600-85153200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:85146000-85153400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:85146800-85153200	Weak transcription	Osteobl	bone
39	chr1:85150800-85153400	Enhancers	Fetal Intestine Small	intestine
40	chr1:85151400-85153200	Weak transcription	Fetal Intestine Large	intestine
41	chr1:85151400-85153600	Weak transcription	Fetal Heart	heart
42	chr1:85151400-85154200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr1:85151400-85154400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:85151800-85153600	Enhancers	Fetal Brain Male	brain
45	chr1:85152000-85154200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr1:85152000-85155000	Active TSS	Brain Angular Gyrus	brain
47	chr1:85152200-85153000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr1:85152200-85153600	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr1:85152200-85154200	Enhancers	Thymus	Thymus
50	chr1:85152400-85153400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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