Variant report

Variant	rs6587606
Chromosome Location	chr1:151580720-151580721
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:29)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:29 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr1:151580695-151581198	MCF-7	breast:	n/a	n/a
2	TCF12	chr1:151580564-151581342	SK-N-SH	brain:	n/a	n/a
3	FOSL2	chr1:151580686-151581236	MCF-7	breast:	n/a	chr1:151580970-151580981
4	POLR2A	chr1:151580659-151581232	SK-N-SH	brain:	n/a	n/a
5	TAF1	chr1:151580658-151581247	PFSK-1	brain:	n/a	n/a
6	RCOR1	chr1:151580678-151581329	IMR90	lung:	n/a	n/a
7	TCF12	chr1:151580571-151581367	SK-N-SH	brain:	n/a	n/a
8	FOSL1	chr1:151580569-151581247	HCT-116	colon:	n/a	n/a
9	POLR2A	chr1:151580598-151581198	SK-N-MC	brain:	n/a	n/a
10	POLR2A	chr1:151580582-151581286	PFSK-1	brain:	n/a	n/a
11	REST	chr1:151580685-151581111	PFSK-1	brain:	n/a	n/a
12	JUN	chr1:151580719-151581311	K562	blood:	n/a	n/a
13	JUND	chr1:151580616-151581401	SK-N-SH	brain:	n/a	chr1:151580969-151580980
14	CEBPB	chr1:151580668-151581259	A549	lung:	n/a	n/a
15	TAF1	chr1:151580701-151581161	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr1:151580720-151581193	HCT-116	colon:	n/a	n/a
17	FOSL2	chr1:151580607-151581275	A549	lung:	n/a	chr1:151580970-151580981
18	FOSL2	chr1:151580709-151581111	HepG2	liver:	n/a	chr1:151580970-151580981
19	JUND	chr1:151580629-151581197	HCT-116	colon:	n/a	chr1:151580969-151580980
20	POLR2A	chr1:151580715-151581177	SK-N-SH	brain:	n/a	n/a
21	JUND	chr1:151580691-151581176	A549	lung:	n/a	chr1:151580969-151580980
22	SP1	chr1:151580600-151581203	A549	lung:	n/a	n/a
23	REST	chr1:151580671-151581102	PFSK-1	brain:	n/a	n/a
24	MAZ	chr1:151580668-151581312	IMR90	lung:	n/a	chr1:151581234-151581243
25	POLR2A	chr1:151580603-151581322	U87	brain:	n/a	n/a
26	POLR2A	chr1:151580504-151581411	PFSK-1	brain:	n/a	n/a
27	SP1	chr1:151580588-151581188	A549	lung:	n/a	n/a
28	HEY1	chr1:151580717-151581161	HepG2	liver:	n/a	n/a
29	FOSL2	chr1:151580714-151581233	MCF-7	breast:	n/a	chr1:151580970-151580981

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:151580708-151580758	HCM	heart:	n/a
2	chr1:151580708-151580758	GM12891	blood:	n/a
3	chr1:151580708-151580758	NH-A	brain:	n/a
4	chr1:151580708-151580758	NHDF-neo	bronchial:	n/a
5	chr1:151580708-151580758	Hepatocyte	liver:	n/a
6	chr1:151580708-151580758	LNCaP	prostate:	n/a
7	chr1:151580708-151580758	H1-hESC	embryonic stem cell:	embryo
8	chr1:151580708-151580758	ProgFib	skin:	n/a
9	chr1:151580708-151580758	RPTEC	kidney:	n/a
10	chr1:151580708-151580758	BJ	skin:	n/a
11	chr1:151580708-151580758	Jurkat	blood:	n/a
12	chr1:151580708-151580758	HAEpiC	amniotic membrane:	n/a
13	chr1:151580708-151580758	MCF10A-Er-Src	breast:	n/a
14	chr1:151580708-151580758	SKMC	muscle:	n/a
15	chr1:151580708-151580758	HCF	heart:	n/a
16	chr1:151580708-151580758	AG04449	skin:	fetal
17	chr1:151580708-151580758	HRCEpiC	kidney:	n/a
18	chr1:151580708-151580758	SAEC	small airway:	n/a
19	chr1:151580708-151580758	MCF-7	breast:	n/a
20	chr1:151580708-151580758	GM19239	blood:	n/a
21	chr1:151580708-151580758	NT2-D1	testis:	n/a
22	chr1:151580708-151580758	U87	brain:	n/a
23	chr1:151580708-151580758	AG09319	gingival:	n/a
24	chr1:151580708-151580758	PFSK-1	brain:	n/a
25	chr1:151580708-151580758	HRPEpiC	eye:	n/a
26	chr1:151580708-151580758	PANC-1	pancreas:	n/a
27	chr1:151580708-151580758	HIPEpiC	eye:	n/a
28	chr1:151580708-151580758	HCPEpiC	choroid plexus:	n/a
29	chr1:151580708-151580758	HMEC	breast:	n/a
30	chr1:151580708-151580758	HCT-116	colon:	n/a
31	chr1:151580708-151580758	HUVEC	blood vessel:	n/a
32	chr1:151580708-151580758	HNPCEpiC	eye:	n/a
33	chr1:151580708-151580758	HPAEpiC	pulmonary alveolar:	n/a
34	chr1:151580708-151580758	HEK293	kidney:	embryo
35	chr1:151580708-151580758	NB4	blood:	n/a
36	chr1:151580708-151580758	AG10803	skin:	n/a
37	chr1:151580708-151580758	GM12878	blood:	n/a
38	chr1:151580708-151580758	HEEpiC	esophagus:	n/a
39	chr1:151580708-151580758	AoSMC	blood vessel:	n/a
40	chr1:151580708-151580758	AG04450	lung:	fetal
41	chr1:151580708-151580758	SK-N-SH	brain:	n/a
42	chr1:151580708-151580758	SK-N-MC	brain:	n/a
43	chr1:151580708-151580758	Hela-S3	cervix:	n/a
44	chr1:151580708-151580758	GM12892	blood:	n/a
45	chr1:151580708-151580758	BE2_C	brain:	n/a
46	chr1:151580708-151580758	HepG2	liver:	n/a
47	chr1:151580708-151580758	CMK	blood:	n/a
48	chr1:151580708-151580758	T-47D	breast:	n/a
49	chr1:151580708-151580758	SK-N-SH_RA	brain:	n/a
50	chr1:151580708-151580758	NHBE	bronchial:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:151549087..151552295-chr1:151579604..151582437,3	MCF-7	breast:
2	chr1:151574917..151577114-chr1:151578095..151581619,4	MCF-7	breast:

No data

Variant related genes	Relation type
SNX27	TF binding region
SNX27	CpG island

Extended variants
information (count: 7 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10888424	0.94[EUR][1000 genomes]
rs12749	0.93[CEU][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs1970568	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6691958	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs6698868	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7528601	0.91[EUR][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	nsv997511	chr1:151491765-151595902	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6587606	BOD1P	trans	parietal	SCAN
rs6587606	LINGO4	cis	cerebellum	SCAN
rs6587606	IVL	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151555400-151580800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:151575400-151580800	Weak transcription	K562	blood
3	chr1:151578200-151581200	Enhancers	Fetal Intestine Small	intestine
4	chr1:151578400-151581400	Enhancers	Fetal Intestine Large	intestine
5	chr1:151578400-151581400	Enhancers	Placenta	Placenta
6	chr1:151578600-151580800	Enhancers	A549	lung
7	chr1:151578600-151581400	Enhancers	HMEC	breast
8	chr1:151578800-151580800	Enhancers	HepG2	liver
9	chr1:151579000-151580800	Enhancers	Hela-S3	cervix
10	chr1:151579200-151580800	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr1:151579400-151581200	Enhancers	NHEK	skin
12	chr1:151579600-151580800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:151579600-151580800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:151579800-151580800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr1:151579800-151581600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:151579800-151583600	Weak transcription	Stomach Mucosa	stomach
17	chr1:151579800-151583800	Weak transcription	Pancreas	Pancrea
18	chr1:151580000-151582600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:151580200-151580800	Bivalent Enhancer	Fetal Muscle Leg	muscle
20	chr1:151580200-151581400	Enhancers	NHDF-Ad	bronchial
21	chr1:151580200-151584000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr1:151580400-151581200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:151580400-151581400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:151580600-151580800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:151580600-151580800	Enhancers	NHLF	lung
26	chr1:151580600-151581000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:151580600-151581000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:151580600-151581000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:151580600-151581000	Weak transcription	Adipose Nuclei	Adipose
30	chr1:151580600-151581000	Active TSS	Osteobl	bone
31	chr1:151580600-151581200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:151580600-151581200	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr1:151580600-151581200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
34	chr1:151580600-151581200	Active TSS	Stomach Smooth Muscle	stomach
35	chr1:151580600-151581200	Enhancers	NH-A	brain
36	chr1:151580600-151581400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:151580600-151581400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:151580600-151581600	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr1:151580600-151581600	Enhancers	Fetal Muscle Trunk	muscle

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