Variant report

Variant	rs3855959
Chromosome Location	chr1:46633874-46633875
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:46593944..46606364-chr1:46632700..46654752,92	MCF-7	breast:
2	chr1:46509224..46511270-chr1:46633534..46635537,2	K562	blood:
3	chr1:46618679..46620713-chr1:46633410..46635446,2	MCF-7	breast:
4	chr1:46621845..46624793-chr1:46632573..46635371,3	MCF-7	breast:
5	chr1:46629247..46631645-chr1:46633727..46635597,2	K562	blood:
6	chr1:46633874..46635736-chr1:46769264..46771947,2	K562	blood:
7	chr1:46622822..46627541-chr1:46631792..46634999,5	K562	blood:
8	chr1:46633292..46635989-chr1:46638272..46640945,3	K562	blood:
9	chr1:46624121..46627541-chr1:46631792..46634999,3	K562	blood:
10	chr1:46590920..46606215-chr1:46630948..46642525,66	MCF-7	breast:

No data

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

Extended variants
information (count: 22 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10493121	0.82[JPT][hapmap]
rs1112471	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12029005	0.94[ASN][1000 genomes]
rs1618281	0.84[JPT][hapmap]
rs3820082	0.86[JPT][hapmap]
rs3845300	0.91[JPT][hapmap]
rs3845301	0.83[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.80[ASN][1000 genomes]
rs6671303	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6686661	0.80[ASN][1000 genomes]
rs7512966	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs7536272	0.91[JPT][hapmap]
rs7552775	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3855959	CCDC163P	cis	lung	GTEx
rs3855959	CCDC163P	cis	Thyroid	GTEx
rs3855959	CCDC163P	cis	Esophagus Muscularis	GTEx
rs3855959	CCDC163P	cis	Esophagus Mucosa	GTEx
rs3855959	MAST2	cis	Artery Tibial	GTEx
rs3855959	CMPK1	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46632600-46634000	Weak transcription	K562	blood
2	chr1:46632600-46635800	Enhancers	Spleen	Spleen
3	chr1:46633000-46634000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:46633000-46634600	Enhancers	Lung	lung
5	chr1:46633200-46634200	Bivalent Enhancer	Adipose Nuclei	Adipose
6	chr1:46633200-46634400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
7	chr1:46633200-46634800	Enhancers	Fetal Thymus	thymus
8	chr1:46633200-46635400	Weak transcription	Gastric	stomach
9	chr1:46633200-46635800	Enhancers	Left Ventricle	heart
10	chr1:46633200-46636800	Weak transcription	Placenta	Placenta
11	chr1:46633200-46636800	Weak transcription	HUVEC	blood vessel
12	chr1:46633200-46637000	Weak transcription	Esophagus	oesophagus
13	chr1:46633200-46637000	Weak transcription	Pancreas	Pancrea
14	chr1:46633200-46637000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:46633200-46637600	Weak transcription	Psoas Muscle	Psoas
16	chr1:46633400-46635800	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr1:46633400-46636800	Weak transcription	Primary B cells from peripheral blood	blood
18	chr1:46633400-46636800	Weak transcription	GM12878-XiMat	blood
19	chr1:46633400-46637200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr1:46633400-46637800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr1:46633400-46638800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:46633400-46638800	Weak transcription	Brain Anterior Caudate	brain
23	chr1:46633400-46638800	Weak transcription	Colon Smooth Muscle	Colon
24	chr1:46633400-46638800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr1:46633600-46634400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:46633600-46639200	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr1:46633800-46634600	Enhancers	Right Atrium	heart
28	chr1:46633800-46635600	Enhancers	Right Ventricle	heart

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