Variant report

Variant	rs4321336
Chromosome Location	chr2:10231633-10231634
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD1	chr2:10231573-10231813	GM12878	blood:	n/a	n/a
2	CTCF	chr2:10231600-10231750	RPTEC	kidney:	n/a	n/a
3	PAX5	chr2:10231153-10231743	GM12878	blood:	n/a	n/a
4	POLR2A	chr2:10231277-10232056	GM19193	blood:	n/a	n/a
5	CTCF	chr2:10231520-10231670	GM12866	blood:	n/a	n/a
6	POLR2A	chr2:10231221-10232112	GM19099	blood:	n/a	n/a
7	ELF1	chr2:10231200-10231907	GM12878	blood:	n/a	n/a
8	ZNF143	chr2:10231470-10232115	GM12878	blood:	n/a	n/a
9	MAX	chr2:10231372-10232035	GM12878	blood:	n/a	n/a
10	POLR2A	chr2:10231242-10232028	GM18526	blood:	n/a	n/a
11	POLR2A	chr2:10231261-10232050	GM18951	blood:	n/a	n/a
12	PAX5	chr2:10231205-10232077	GM12878	blood:	n/a	n/a
13	TCF3	chr2:10231618-10232080	GM12878	blood:	n/a	n/a
14	CTCF	chr2:10231580-10231730	GM06990	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:10231621-10231671	HCF	heart:	n/a
2	chr2:10231621-10231671	HCT-116	colon:	n/a
3	chr2:10231621-10231671	HRE	kidney:	n/a
4	chr2:10231621-10231671	SKMC	muscle:	n/a
5	chr2:10231621-10231671	AG04449	skin:	fetal
6	chr2:10231621-10231671	HEK293	kidney:	embryo
7	chr2:10231621-10231671	GM12878	blood:	n/a
8	chr2:10231621-10231671	AG09309	skin:	n/a
9	chr2:10231621-10231671	A549	lung:	n/a
10	chr2:10231621-10231671	ProgFib	skin:	n/a
11	chr2:10231621-10231671	SAEC	small airway:	n/a
12	chr2:10231621-10231671	Caco-2	colon:	n/a
13	chr2:10231621-10231671	PFSK-1	brain:	n/a
14	chr2:10231621-10231671	HNPCEpiC	eye:	n/a
15	chr2:10231621-10231671	HRCEpiC	kidney:	n/a
16	chr2:10231621-10231671	GM12892	blood:	n/a
17	chr2:10231621-10231671	Hepatocyte	liver:	n/a
18	chr2:10231621-10231671	HRPEpiC	eye:	n/a
19	chr2:10231621-10231671	H1-hESC	embryonic stem cell:	embryo
20	chr2:10231621-10231671	HAEpiC	amniotic membrane:	n/a
21	chr2:10231621-10231671	SK-N-MC	brain:	n/a
22	chr2:10231621-10231671	CMK	blood:	n/a
23	chr2:10231621-10231671	PrEC	prostate:	n/a
24	chr2:10231621-10231671	AoSMC	blood vessel:	n/a
25	chr2:10231621-10231671	HIPEpiC	eye:	n/a
26	chr2:10231621-10231671	ECC-1	luminal epithelium:	n/a
27	chr2:10231621-10231671	PANC-1	pancreas:	n/a
28	chr2:10231621-10231671	BE2_C	brain:	n/a
29	chr2:10231621-10231671	BJ	skin:	n/a
30	chr2:10231621-10231671	HCM	heart:	n/a
31	chr2:10231621-10231671	HUVEC	blood vessel:	n/a
32	chr2:10231621-10231671	AG10803	skin:	n/a
33	chr2:10231621-10231671	MCF10A-Er-Src	breast:	n/a
34	chr2:10231621-10231671	GM19239	blood:	n/a
35	chr2:10231621-10231671	K562	blood:	n/a
36	chr2:10231621-10231671	AG04450	lung:	fetal
37	chr2:10231621-10231671	AG09319	gingival:	n/a
38	chr2:10231621-10231671	LNCaP	prostate:	n/a
39	chr2:10231621-10231671	GM12891	blood:	n/a
40	chr2:10231621-10231671	ovcar-3	ovarian:	n/a
41	chr2:10231621-10231671	HCPEpiC	choroid plexus:	n/a
42	chr2:10231621-10231671	GM06990	blood:	n/a
43	chr2:10231621-10231671	MCF-7	breast:	n/a
44	chr2:10231621-10231671	HEEpiC	esophagus:	n/a
45	chr2:10231621-10231671	Jurkat	blood:	n/a
46	chr2:10231621-10231671	Hela-S3	cervix:	n/a
47	chr2:10231621-10231671	NHDF-neo	bronchial:	n/a
48	chr2:10231621-10231671	NHBE	bronchial:	n/a
49	chr2:10231621-10231671	NT2-D1	testis:	n/a
50	chr2:10231621-10231671	SK-N-SH_RA	brain:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:10231244..10232877-chr2:10442178..10444035,2	K562	blood:
2	chr2:10229570..10233123-chr2:10259464..10263291,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000212558	TF binding region
ENSG00000212558	CpG island
ENSG00000272524	Chromatin interaction
ENSG00000171848	Chromatin interaction
ENSG00000115756	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10177872	1.00[ASN][1000 genomes]
rs10929632	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11886661	1.00[ASN][1000 genomes]
rs12992149	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13400128	1.00[ASN][1000 genomes]
rs3935840	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4302193	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4485541	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4569449	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669527	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669528	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6432058	1.00[ASN][1000 genomes]
rs6432060	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72786623	1.00[ASN][1000 genomes]
rs72786624	1.00[ASN][1000 genomes]
rs7587317	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7587529	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602408	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv828297	chr2:10109299-10236332	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1007965	chr2:10154960-10276125	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers 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
5	nsv1014790	chr2:10156968-10274855	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
6	nsv999019	chr2:10157762-10273232	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
7	nsv873633	chr2:10175442-10266563	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
8	nsv1010706	chr2:10189219-10266995	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4321336	CYS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10230800-10232000	Flanking Active TSS	GM12878-XiMat	blood
2	chr2:10231000-10232000	Bivalent Enhancer	Fetal Muscle Leg	muscle
3	chr2:10231200-10231800	Bivalent Enhancer	Fetal Intestine Small	intestine
4	chr2:10231200-10232000	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr2:10231200-10232000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
6	chr2:10231200-10232000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr2:10231200-10232000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:10231200-10232000	Enhancers	Pancreas	Pancrea
9	chr2:10231200-10232200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
10	chr2:10231400-10231800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
11	chr2:10231400-10231800	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:10231400-10231800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
13	chr2:10231400-10231800	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
14	chr2:10231400-10231800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
15	chr2:10231400-10231800	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr2:10231400-10231800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:10231400-10231800	Bivalent/Poised TSS	Brain Anterior Caudate	brain
18	chr2:10231400-10231800	Bivalent Enhancer	Brain Germinal Matrix	brain
19	chr2:10231400-10231800	Bivalent Enhancer	Brain Hippocampus Middle	brain
20	chr2:10231400-10231800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
21	chr2:10231400-10231800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
22	chr2:10231400-10231800	Bivalent Enhancer	Fetal Thymus	thymus
23	chr2:10231400-10231800	Flanking Active TSS	Gastric	stomach
24	chr2:10231400-10231800	Bivalent Enhancer	Left Ventricle	heart
25	chr2:10231400-10231800	Flanking Active TSS	Ovary	ovary
26	chr2:10231400-10231800	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr2:10231400-10231800	Active TSS	Right Atrium	heart
28	chr2:10231400-10231800	Flanking Active TSS	Right Ventricle	heart
29	chr2:10231400-10231800	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
30	chr2:10231400-10231800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
31	chr2:10231400-10232000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr2:10231400-10232000	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
33	chr2:10231400-10232000	Flanking Active TSS	Primary B cells from peripheral blood	blood
34	chr2:10231400-10232000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
35	chr2:10231400-10232000	Bivalent/Poised TSS	Primary T helper naive cells fromperipheralblood	blood
36	chr2:10231400-10232000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
37	chr2:10231400-10232000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr2:10231400-10232000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr2:10231400-10232000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:10231400-10232000	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr2:10231400-10232000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr2:10231400-10232000	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
43	chr2:10231400-10232000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
44	chr2:10231400-10232000	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
45	chr2:10231400-10232000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
46	chr2:10231400-10232000	ZNF genes & repeats	Lung	lung
47	chr2:10231400-10232000	Bivalent/Poised TSS	Psoas Muscle	Psoas
48	chr2:10231400-10232000	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
49	chr2:10231400-10232000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
50	chr2:10231400-10232000	Bivalent/Poised TSS	Thymus	Thymus

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