Variant report

Variant	rs55884940
Chromosome Location	chr1:46639016-46639017
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:46638894-46639844	H1-neurons	neurons:	n/a	n/a
2	JUN	chr1:46638774-46641517	K562	blood:	n/a	chr1:46640276-46640289 chr1:46639425-46639434 chr1:46639421-46639434
3	RAD21	chr1:46638993-46639537	H1-hESC	embryonic stem cell:	n/a	chr1:46639304-46639316 chr1:46639319-46639333 chr1:46639306-46639316
4	REST	chr1:46638677-46639973	H1-neurons	neurons:	n/a	chr1:46639593-46639606
5	ZNF263	chr1:46638656-46639608	HEK293-T-REx	kidney:	n/a	chr1:46639343-46639352 chr1:46639347-46639368
6	CTCF	chr1:46638927-46639501	K562	blood:	n/a	chr1:46639319-46639332
7	CTCF	chr1:46638980-46639130	HL-60	blood:	n/a	n/a
8	CTCF	chr1:46638960-46639110	GM12867	blood:	n/a	n/a
9	CTCF	chr1:46638980-46639130	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:46638844-46639973	H1-neurons	neurons:	n/a	n/a
11	CTCF	chr1:46638940-46639090	HCFaa	heart:	n/a	n/a
12	CTCF	chr1:46639000-46639150	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:46638980..46642595-chr1:46645721..46649189,9	MCF-7	breast:
2	chr1:46593944..46606364-chr1:46632700..46654752,92	MCF-7	breast:
3	chr1:46639014..46640668-chr1:46643175..46645407,2	K562	blood:
4	chr1:46636993..46639249-chr1:46644481..46646542,2	MCF-7	breast:
5	chr1:45985928..45987580-chr1:46638994..46641452,2	K562	blood:
6	chr1:45985928..45987580-chr1:46638994..46641452,3	K562	blood:
7	chr1:46636697..46639165-chr1:46652056..46653716,2	MCF-7	breast:
8	chr1:46635707..46641847-chr1:46658318..46665376,6	K562	blood:
9	chr1:46546706..46549522-chr1:46637741..46639306,2	MCF-7	breast:
10	chr1:46638350..46640274-chr1:46653055..46655408,2	K562	blood:
11	chr1:46501344..46502975-chr1:46637425..46639494,2	MCF-7	breast:
12	chr1:46502253..46502993-chr1:46638861..46639852,3	K562	blood:
13	chr1:46501684..46503933-chr1:46638611..46640285,2	K562	blood:
14	chr1:46590920..46606215-chr1:46630948..46642525,66	MCF-7	breast:

Variant related genes	Relation type
TSPAN1	TF binding region
ENSG00000085998	Chromatin interaction
ENSG00000117472	Chromatin interaction
ENSG00000117450	Chromatin interaction
ENSG00000117461	Chromatin interaction
ENSG00000227857	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12076680	1.00[ASN][1000 genomes]
rs12123115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12131635	0.97[EUR][1000 genomes]
rs72677567	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7519183	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9660699	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
7	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
8	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
9	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55884940	NSUN4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46633600-46639200	Enhancers	Skeletal Muscle Male	skeletal muscle
2	chr1:46635600-46642200	Enhancers	Lung	lung
3	chr1:46636800-46639400	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr1:46636800-46641200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:46636800-46641400	Enhancers	Placenta	Placenta
6	chr1:46636800-46642200	Enhancers	Left Ventricle	heart
7	chr1:46636800-46642400	Enhancers	Right Atrium	heart
8	chr1:46636800-46642400	Enhancers	Right Ventricle	heart
9	chr1:46637000-46641200	Enhancers	Fetal Muscle Leg	muscle
10	chr1:46637200-46639800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:46637400-46639200	Weak transcription	HSMM	muscle
12	chr1:46637800-46639400	Enhancers	Adipose Nuclei	Adipose
13	chr1:46637800-46639400	Weak transcription	Duodenum Mucosa	Duodenum
14	chr1:46637800-46639600	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr1:46637800-46640400	Weak transcription	Small Intestine	intestine
16	chr1:46637800-46649600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr1:46638000-46639200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:46638000-46639200	Weak transcription	Colonic Mucosa	Colon
19	chr1:46638000-46639200	Weak transcription	Esophagus	oesophagus
20	chr1:46638000-46639200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr1:46638000-46639400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr1:46638000-46639800	Weak transcription	Stomach Mucosa	stomach
23	chr1:46638000-46639800	Weak transcription	NHEK	skin
24	chr1:46638000-46640000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr1:46638000-46640600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:46638000-46645000	Weak transcription	HMEC	breast
27	chr1:46638200-46639200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:46638200-46639200	Weak transcription	Pancreas	Pancrea
29	chr1:46638400-46639600	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr1:46638600-46639800	Enhancers	Primary B cells from peripheral blood	blood
31	chr1:46638600-46641400	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr1:46638600-46641400	Enhancers	Fetal Heart	heart
33	chr1:46638800-46639200	Enhancers	Brain Cingulate Gyrus	brain
34	chr1:46638800-46639400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:46638800-46639400	Enhancers	Brain Anterior Caudate	brain
36	chr1:46638800-46639400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:46638800-46639400	Enhancers	Colon Smooth Muscle	Colon
38	chr1:46638800-46639600	Enhancers	Brain Angular Gyrus	brain
39	chr1:46638800-46639800	Flanking Active TSS	Rectal Smooth Muscle	rectum
40	chr1:46638800-46640000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:46638800-46640000	Bivalent Enhancer	HepG2	liver
42	chr1:46638800-46640000	Enhancers	HSMMtube	muscle
43	chr1:46638800-46640200	Enhancers	K562	blood
44	chr1:46638800-46640400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:46638800-46640800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr1:46638800-46640800	Enhancers	Osteobl	bone
47	chr1:46638800-46641000	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr1:46638800-46641000	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr1:46638800-46641000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:46638800-46641200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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