Variant report

Variant	rs2786098
Chromosome Location	chr1:197325908-197325909
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr1:197325708-197326596	SK-N-SH	brain:	n/a	n/a
2	RAD21	chr1:197325863-197326670	SK-N-SH	brain:	n/a	n/a
3	RAD21	chr1:197325856-197326491	SK-N-SH_RA	brain:	n/a	n/a
4	RAD21	chr1:197325838-197326588	HCT-116	colon:	n/a	n/a
5	RAD21	chr1:197325893-197326575	MCF-7	breast:	n/a	n/a
6	RAD21	chr1:197325875-197326510	HCT-116	colon:	n/a	n/a
7	CTCF	chr1:197325904-197326573	MCF-7	breast:	n/a	n/a
8	CTCF	chr1:197325780-197325930	HFF	foreskin:	n/a	n/a
9	CTCF	chr1:197325862-197326576	A549	lung:	n/a	n/a
10	CTCF	chr1:197325831-197326690	SK-N-SH	brain:	n/a	n/a
11	RAD21	chr1:197325870-197326505	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:197319425..197321252-chr1:197323446..197325972,2	MCF-7	breast:
2	chr1:197296672..197297586-chr1:197325782..197326703,4	K562	blood:
3	chr1:197296323..197297408-chr1:197325745..197326738,7	MCF-7	breast:
4	chr1:197148748..197149958-chr1:197325829..197326773,3	MCF-7	breast:
5	chr1:197193137..197194020-chr1:197325790..197326689,5	MCF-7	breast:
6	chr1:197324727..197326366-chr1:197333265..197336243,2	K562	blood:
7	chr1:197149241..197150078-chr1:197325625..197326699,7	K562	blood:

No data

Variant related genes	Relation type
CRB1	TF binding region

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

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10801603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10922234	0.86[CEU][hapmap];0.81[TSI][hapmap]
rs12126335	0.94[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs12134409	0.95[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs12563307	0.86[CEU][hapmap]
rs1337167	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.80[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1337168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17554990	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs17618358	0.94[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs2476019	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs2476021	0.84[EUR][1000 genomes]
rs2476023	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.85[YRI][hapmap]
rs2494269	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs2759656	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs2759659	0.83[EUR][1000 genomes]
rs2759661	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs2786100	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2786101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2786103	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2786116	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2786117	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2786119	1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.80[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2821101	0.83[EUR][1000 genomes]
rs2821107	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2821115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2821116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2821117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2821125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2821132	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs3122635	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3122636	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4915231	0.93[ASN][1000 genomes]
rs4915525	0.92[ASN][1000 genomes]
rs4915526	0.92[ASN][1000 genomes]
rs6428397	0.94[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs6664399	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6685222	0.95[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs7551088	0.88[ASN][1000 genomes]
rs949571	0.94[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1014039	chr1:197311285-197529212	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Asthma	20032318	GWAS catalog

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197316200-197329200	Weak transcription	Brain Substantia Nigra	brain
2	chr1:197324000-197338800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr1:197324000-197347000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:197324600-197327400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:197325600-197329200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr1:197325800-197326400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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