Variant report

Variant	rs3845300
Chromosome Location	chr1:46635149-46635150
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:46635040..46637380-chr1:46652840..46654559,2	MCF-7	breast:
2	chr1:46634262..46636688-chr1:46646311..46648808,2	MCF-7	breast:
3	chr1:46593944..46606364-chr1:46632700..46654752,92	MCF-7	breast:
4	chr1:46634943..46636544-chr1:46711227..46713970,2	K562	blood:
5	chr1:46509224..46511270-chr1:46633534..46635537,2	K562	blood:
6	chr1:46618679..46620713-chr1:46633410..46635446,2	MCF-7	breast:
7	chr1:46621845..46624793-chr1:46632573..46635371,3	MCF-7	breast:
8	chr1:46629247..46631645-chr1:46633727..46635597,2	K562	blood:
9	chr1:46633874..46635736-chr1:46769264..46771947,2	K562	blood:
10	chr1:46633292..46635989-chr1:46638272..46640945,3	K562	blood:
11	chr1:46590920..46606215-chr1:46630948..46642525,66	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000117472	Chromatin interaction
ENSG00000132128	Chromatin interaction
ENSG00000173660	Chromatin interaction
ENSG00000117461	Chromatin interaction
ENSG00000085999	Chromatin interaction
ENSG00000227857	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10493121	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1112471	0.81[JPT][hapmap]
rs11211258	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11211259	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12029005	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12029134	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12029936	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12064594	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12134419	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1618281	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1620877	0.88[ASN][1000 genomes]
rs3753363	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3820082	0.82[ASW][hapmap];0.89[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3845301	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs3855959	0.91[JPT][hapmap]
rs6661071	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6671303	0.91[JPT][hapmap]
rs6686661	0.82[ASN][1000 genomes]
rs7512966	0.88[CEU][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7536272	0.84[CEU][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs785475	0.89[MEX][hapmap];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
2	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
3	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
5	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
6	esv2754420	chr1:46461580-46635180	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv1006747	chr1:46476089-46655484	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv534947	chr1:46476089-46655484	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv1006530	chr1:46544842-46655484	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
10	nsv534949	chr1:46544842-46655484	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3845300	IPP	cis	lymphoblastoid	seeQTL
rs3845300	CMPK1	cis	cerebellum	SCAN
rs3845300	MPL	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46632600-46635800	Enhancers	Spleen	Spleen
2	chr1:46633200-46635400	Weak transcription	Gastric	stomach
3	chr1:46633200-46635800	Enhancers	Left Ventricle	heart
4	chr1:46633200-46636800	Weak transcription	Placenta	Placenta
5	chr1:46633200-46636800	Weak transcription	HUVEC	blood vessel
6	chr1:46633200-46637000	Weak transcription	Esophagus	oesophagus
7	chr1:46633200-46637000	Weak transcription	Pancreas	Pancrea
8	chr1:46633200-46637000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:46633200-46637600	Weak transcription	Psoas Muscle	Psoas
10	chr1:46633400-46635800	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr1:46633400-46636800	Weak transcription	Primary B cells from peripheral blood	blood
12	chr1:46633400-46636800	Weak transcription	GM12878-XiMat	blood
13	chr1:46633400-46637200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr1:46633400-46637800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:46633400-46638800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:46633400-46638800	Weak transcription	Brain Anterior Caudate	brain
17	chr1:46633400-46638800	Weak transcription	Colon Smooth Muscle	Colon
18	chr1:46633400-46638800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr1:46633600-46639200	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr1:46633800-46635600	Enhancers	Right Ventricle	heart
21	chr1:46634000-46636800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:46634400-46636800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:46634400-46638800	Weak transcription	K562	blood
24	chr1:46634600-46635600	Weak transcription	Lung	lung
25	chr1:46634800-46636800	Weak transcription	Fetal Thymus	thymus
26	chr1:46635000-46635800	Enhancers	Right Atrium	heart

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