Variant report

Variant	rs56335231
Chromosome Location	chr1:247500399-247500400
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:247497896..247501644-chr1:247501987..247504336,4	MCF-7	breast:
2	chr1:247498783..247501107-chr1:247612451..247615319,2	K562	blood:
3	chr1:247374235..247377046-chr1:247498080..247500631,2	K562	blood:

Variant related genes	Relation type
ENSG00000177535	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10754545	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1192833	0.87[ASN][1000 genomes]
rs12023326	0.88[ASN][1000 genomes]
rs12023478	0.86[ASN][1000 genomes]
rs12026978	0.88[ASN][1000 genomes]
rs12027522	0.91[ASN][1000 genomes]
rs12034916	0.89[ASN][1000 genomes]
rs12034919	0.89[ASN][1000 genomes]
rs12035371	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12035515	0.81[ASN][1000 genomes]
rs12047860	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12048553	0.92[ASN][1000 genomes]
rs12404914	0.89[ASN][1000 genomes]
rs17664745	0.88[ASN][1000 genomes]
rs3850825	0.88[ASN][1000 genomes]
rs56013900	0.88[ASN][1000 genomes]
rs56322048	0.89[ASN][1000 genomes]
rs56366903	0.94[ASN][1000 genomes]
rs56396334	0.89[ASN][1000 genomes]
rs56740645	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6426239	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6690864	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6697861	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7522071	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	esv3411043	chr1:247382851-247517729	Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
3	esv3378684	chr1:247382994-247518438	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
4	nsv833137	chr1:247437317-247607428	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	n/a
5	nsv873439	chr1:247486736-247549220	Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	n/a
6	esv1799864	chr1:247494789-247500650	Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56335231	ZNF496	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247496200-247503000	Weak transcription	Aorta	Aorta
2	chr1:247496400-247501600	Enhancers	Primary hematopoietic stem cells	blood
3	chr1:247496400-247511000	Weak transcription	Primary B cells from cord blood	blood
4	chr1:247496600-247500400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr1:247496600-247501000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:247496600-247501000	Weak transcription	NHDF-Ad	bronchial
7	chr1:247496600-247505800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:247496600-247506000	Weak transcription	HSMMtube	muscle
9	chr1:247496600-247511000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr1:247496800-247500400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:247496800-247500800	Weak transcription	Ovary	ovary
12	chr1:247496800-247501200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:247496800-247501200	Genic enhancers	Fetal Muscle Leg	muscle
14	chr1:247496800-247501400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:247496800-247502000	Weak transcription	HSMM	muscle
16	chr1:247496800-247502200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:247496800-247503000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:247496800-247507200	Weak transcription	Fetal Intestine Large	intestine
19	chr1:247496800-247510200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr1:247497000-247501600	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr1:247497000-247503000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:247497000-247504000	Weak transcription	Stomach Mucosa	stomach
23	chr1:247497000-247511200	Weak transcription	Esophagus	oesophagus
24	chr1:247497200-247500800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
25	chr1:247497200-247500800	Weak transcription	Brain Hippocampus Middle	brain
26	chr1:247497200-247502200	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr1:247497200-247503000	Weak transcription	NHEK	skin
28	chr1:247497200-247505800	Weak transcription	Brain Substantia Nigra	brain
29	chr1:247497200-247506200	Weak transcription	HMEC	breast
30	chr1:247497200-247509800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:247497200-247516000	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr1:247497400-247500600	Weak transcription	Fetal Brain Male	brain
33	chr1:247497400-247503000	Weak transcription	Duodenum Mucosa	Duodenum
34	chr1:247497400-247511200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:247497400-247511400	Weak transcription	Primary T cells from cord blood	blood
36	chr1:247497800-247501400	Enhancers	H1 Cell Line	embryonic stem cell
37	chr1:247497800-247502800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:247497800-247506400	Weak transcription	GM12878-XiMat	blood
39	chr1:247498000-247500400	Weak transcription	NHLF	lung
40	chr1:247498000-247502800	Weak transcription	Hela-S3	cervix
41	chr1:247498200-247501400	Weak transcription	HepG2	liver
42	chr1:247498200-247501800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr1:247498200-247501800	Weak transcription	Psoas Muscle	Psoas
44	chr1:247498400-247500600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr1:247498400-247501200	Enhancers	K562	blood
46	chr1:247498400-247501600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr1:247498400-247502000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:247498400-247503000	Weak transcription	A549	lung
49	chr1:247498400-247503200	Weak transcription	Fetal Intestine Small	intestine
50	chr1:247498600-247500600	Weak transcription	Brain Angular Gyrus	brain

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