Variant report

Variant	rs56873377
Chromosome Location	chr1:70672605-70672606
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF384	chr1:70672211-70672792	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:70670191..70673421-chr1:70819814..70822311,3	K562	blood:
2	chr1:70668667..70673217-chr1:70684547..70688689,8	K562	blood:
3	chr1:70667153..70674800-chr1:70681943..70693478,26	K562	blood:
4	chr1:70669751..70673129-chr1:70685079..70688457,4	MCF-7	breast:
5	chr1:70671444..70673368-chr1:70706387..70708615,2	K562	blood:

No data

Variant related genes	Relation type
LRRC40	TF binding region
ENSG00000197568	Chromatin interaction
ENSG00000118454	Chromatin interaction
ENSG00000228988	Chromatin interaction
ENSG00000116754	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1412867	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17131236	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17131238	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17131241	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34121744	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35522955	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3753818	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs476591	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs522320	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs549843	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56299138	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57098486	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs587567	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60409157	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60598073	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs610953	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61785267	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61785269	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61785270	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61785272	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs632047	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs651717	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs666163	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6664084	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6664480	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6666941	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6700543	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs676753	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74085998	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7533067	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1798518	chr1:70604106-70723347	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv1797140	chr1:70604106-70724622	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv870841	chr1:70612416-70696554	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv3363438	chr1:70655980-70675467	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56873377	SFRS11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70669200-70673000	Active TSS	K562	blood
2	chr1:70669400-70672800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:70669400-70672800	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr1:70669600-70672800	Active TSS	GM12878-XiMat	blood
5	chr1:70669800-70672800	Active TSS	HMEC	breast
6	chr1:70669800-70673200	Active TSS	A549	lung
7	chr1:70670000-70672800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:70670000-70672800	Active TSS	NH-A	brain
9	chr1:70670000-70673000	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr1:70670200-70672800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:70670200-70672800	Active TSS	Fetal Intestine Large	intestine
12	chr1:70670200-70672800	Active TSS	Right Ventricle	heart
13	chr1:70670200-70672800	Active TSS	Hela-S3	cervix
14	chr1:70670200-70672800	Active TSS	HSMM	muscle
15	chr1:70670200-70673000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:70670200-70673000	Active TSS	NHLF	lung
17	chr1:70670400-70672800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:70670400-70672800	Active TSS	Fetal Kidney	kidney
19	chr1:70670400-70673000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:70670400-70673000	Active TSS	HSMMtube	muscle
21	chr1:70670600-70672800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:70670600-70672800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:70670600-70672800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:70670600-70672800	Active TSS	Stomach Smooth Muscle	stomach
25	chr1:70670600-70673400	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr1:70671200-70672800	Active TSS	Brain Germinal Matrix	brain
27	chr1:70671600-70673200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:70671600-70673400	Active TSS	Right Atrium	heart
29	chr1:70671800-70672800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:70671800-70672800	Active TSS	HepG2	liver
31	chr1:70671800-70673000	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr1:70671800-70673400	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr1:70671800-70673400	Weak transcription	Gastric	stomach
34	chr1:70672000-70672800	Weak transcription	Lung	lung
35	chr1:70672000-70672800	Weak transcription	Pancreas	Pancrea
36	chr1:70672000-70673000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:70672000-70673000	Flanking Active TSS	Liver	Liver
38	chr1:70672000-70686200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr1:70672000-70687000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:70672200-70672800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
41	chr1:70672200-70672800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr1:70672200-70673000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr1:70672200-70673000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr1:70672200-70673000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
45	chr1:70672200-70673000	Flanking Active TSS	Thymus	Thymus
46	chr1:70672200-70673000	Flanking Active TSS	HUVEC	blood vessel
47	chr1:70672200-70673200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:70672200-70673200	Enhancers	Primary B cells from peripheral blood	blood
49	chr1:70672200-70673200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
50	chr1:70672200-70673200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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