Variant report

Variant	rs11163975
Chromosome Location	chr1:84944363-84944364
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GABPA	chr1:84944220-84945464	HL-60	blood:	n/a	chr1:84945217-84945228 chr1:84945219-84945228
2	POLR2A	chr1:84944349-84944483	Gliobla	brain:	n/a	n/a
3	POLR2A	chr1:84944352-84944547	HepG2	liver:	n/a	n/a
4	GABPA	chr1:84944233-84945704	A549	lung:	n/a	chr1:84945217-84945228 chr1:84945219-84945228
5	HCFC1	chr1:84944333-84946183	Hela-S3	cervix:	n/a	n/a
6	NR2C2	chr1:84944196-84945416	GM12878	blood:	n/a	chr1:84944883-84944890
7	MAX	chr1:84944328-84945774	HCT-116	colon:	n/a	chr1:84945328-84945339 chr1:84945327-84945336 chr1:84945201-84945211 chr1:84945330-84945339 chr1:84945331-84945338 chr1:84945327-84945342 chr1:84945329-84945339
8	NR2C2	chr1:84944328-84945549	Hela-S3	cervix:	n/a	chr1:84944883-84944890
9	GABPA	chr1:84944345-84945646	SK-N-SH	brain:	n/a	chr1:84945217-84945228 chr1:84945219-84945228
10	GABPA	chr1:84944209-84945846	MCF-7	breast:	n/a	chr1:84945217-84945228 chr1:84945219-84945228
11	CBX3	chr1:84944362-84945199	K562	blood:	n/a	n/a
12	SREBP2	chr1:84944018-84946811	GM12878	blood:	n/a	n/a
13	CBX3	chr1:84944313-84945655	K562	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:84944363-84944413	HAEpiC	amniotic membrane:	n/a
2	chr1:84944363-84944413	MCF10A-Er-Src	breast:	n/a
3	chr1:84944363-84944413	HNPCEpiC	eye:	n/a
4	chr1:84944363-84944413	LNCaP	prostate:	n/a
5	chr1:84944363-84944413	HRE	kidney:	n/a
6	chr1:84944363-84944413	BJ	skin:	n/a
7	chr1:84944363-84944413	SK-N-MC	brain:	n/a
8	chr1:84944363-84944413	HepG2	liver:	n/a
9	chr1:84944363-84944413	GM19239	blood:	n/a
10	chr1:84944363-84944413	T-47D	breast:	n/a
11	chr1:84944363-84944413	H1-hESC	embryonic stem cell:	embryo
12	chr1:84944363-84944413	ECC-1	luminal epithelium:	n/a
13	chr1:84944363-84944413	HUVEC	blood vessel:	n/a
14	chr1:84944363-84944413	Caco-2	colon:	n/a
15	chr1:84944363-84944413	GM12892	blood:	n/a
16	chr1:84944363-84944413	AoSMC	blood vessel:	n/a
17	chr1:84944363-84944413	U87	brain:	n/a
18	chr1:84944363-84944413	SKMC	muscle:	n/a
19	chr1:84944363-84944413	HEEpiC	esophagus:	n/a
20	chr1:84944363-84944413	ProgFib	skin:	n/a
21	chr1:84944363-84944413	HL-60	blood:	n/a
22	chr1:84944363-84944413	NHDF-neo	bronchial:	n/a
23	chr1:84944363-84944413	Jurkat	blood:	n/a
24	chr1:84944363-84944413	HEK293	kidney:	embryo
25	chr1:84944363-84944413	K562	blood:	n/a
26	chr1:84944363-84944413	HRCEpiC	kidney:	n/a
27	chr1:84944363-84944413	HCM	heart:	n/a
28	chr1:84944363-84944413	NH-A	brain:	n/a
29	chr1:84944363-84944413	HMEC	breast:	n/a
30	chr1:84944363-84944413	AG09319	gingival:	n/a
31	chr1:84944363-84944413	RPTEC	kidney:	n/a
32	chr1:84944363-84944413	IMR90	lung:	fetal
33	chr1:84944363-84944413	PFSK-1	brain:	n/a
34	chr1:84944363-84944413	GM12878	blood:	n/a
35	chr1:84944363-84944413	PrEC	prostate:	n/a
36	chr1:84944363-84944413	SK-N-SH_RA	brain:	n/a
37	chr1:84944363-84944413	NT2-D1	testis:	n/a
38	chr1:84944363-84944413	GM12891	blood:	n/a
39	chr1:84944363-84944413	HCPEpiC	choroid plexus:	n/a
40	chr1:84944363-84944413	AG04450	lung:	fetal
41	chr1:84944363-84944413	AG09309	skin:	n/a
42	chr1:84944363-84944413	BE2_C	brain:	n/a
43	chr1:84944363-84944413	HCT-116	colon:	n/a
44	chr1:84944363-84944413	HRPEpiC	eye:	n/a
45	chr1:84944363-84944413	AG10803	skin:	n/a
46	chr1:84944363-84944413	PANC-1	pancreas:	n/a
47	chr1:84944363-84944413	NHBE	bronchial:	n/a
48	chr1:84944363-84944413	ovcar-3	ovarian:	n/a
49	chr1:84944363-84944413	SAEC	small airway:	n/a
50	chr1:84944363-84944413	HPAEpiC	pulmonary alveolar:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:84943777..84946552-chr1:84970497..84973179,2	MCF-7	breast:
2	chr1:84944342..84945178-chr1:114354948..114355466,2	Hela-S3	cervix:
3	chr1:84943714..84946459-chr1:85038706..85040687,2	K562	blood:
4	chr1:84943703..84948095-chr1:85037647..85043843,8	K562	blood:
5	chr1:84920904..84923414-chr1:84941843..84944839,2	K562	blood:
6	chr1:84928129..84930451-chr1:84943094..84944929,2	MCF-7	breast:

No data

Variant related genes	Relation type
RPF1	TF binding region
RPF1	CpG island
ENSG00000081019	Chromatin interaction
ENSG00000117151	Chromatin interaction
ENSG00000231128	Chromatin interaction
ENSG00000174021	Chromatin interaction
ENSG00000122432	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10493754	0.94[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10874449	0.93[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11163973	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11163974	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11163976	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11163982	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11163985	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11163986	0.93[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11163987	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11163993	0.93[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12075532	0.93[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13093	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17110164	0.91[ASN][1000 genomes]
rs17110485	0.91[ASN][1000 genomes]
rs17110590	0.91[ASN][1000 genomes]
rs56876287	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6658034	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658974	0.91[ASN][1000 genomes]
rs6660306	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6662644	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6662683	0.91[ASN][1000 genomes]
rs6666052	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6666572	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668752	0.91[ASN][1000 genomes]
rs6676502	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6684882	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6701280	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6704452	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72948416	0.96[ASN][1000 genomes]
rs7524576	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7539413	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7541850	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7541909	0.91[ASN][1000 genomes]
rs7547208	0.91[ASN][1000 genomes]
rs7551329	1.00[ASN][1000 genomes]
rs7555773	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7555821	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830437	chr1:84837524-85001269	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84943800-84944800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
2	chr1:84944000-84944400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr1:84944000-84944400	Flanking Bivalent TSS/Enh	Dnd41	blood
4	chr1:84944000-84945000	ZNF genes & repeats	Placenta	Placenta
5	chr1:84944000-84945800	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr1:84944200-84944400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:84944200-84944400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:84944200-84944400	Active TSS	Primary T killer memory cells from peripheral blood	blood
9	chr1:84944200-84944400	Active TSS	Adipose Nuclei	Adipose
10	chr1:84944200-84944400	Active TSS	Brain Hippocampus Middle	brain
11	chr1:84944200-84944400	Bivalent Enhancer	Duodenum Mucosa	Duodenum
12	chr1:84944200-84944400	Enhancers	Left Ventricle	heart
13	chr1:84944200-84944400	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
14	chr1:84944200-84944400	Enhancers	Rectal Smooth Muscle	rectum
15	chr1:84944200-84944400	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
16	chr1:84944200-84944400	Active TSS	Monocytes-CD14+_RO01746	blood
17	chr1:84944200-84944400	Enhancers	NHEK	skin
18	chr1:84944200-84944600	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:84944200-84944600	Flanking Active TSS	Brain Cingulate Gyrus	brain
20	chr1:84944200-84944600	Flanking Active TSS	Colon Smooth Muscle	Colon
21	chr1:84944200-84944800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
22	chr1:84944200-84944800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
23	chr1:84944200-84944800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr1:84944200-84944800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr1:84944200-84944800	ZNF genes & repeats	Fetal Intestine Small	intestine
26	chr1:84944200-84944800	Bivalent/Poised TSS	Fetal Lung	lung
27	chr1:84944200-84944800	ZNF genes & repeats	GM12878-XiMat	blood
28	chr1:84944200-84945000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:84944200-84945200	Active TSS	Skeletal Muscle Female	skeletal muscle
30	chr1:84944200-84945400	Active TSS	Primary neutrophils fromperipheralblood	blood
31	chr1:84944200-84945800	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr1:84944200-84946000	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr1:84944200-84946200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:84944200-84946200	Active TSS	Muscle Satellite Cultured Cells	--
35	chr1:84944200-84946200	Active TSS	A549	lung
36	chr1:84944200-84946400	Active TSS	Stomach Smooth Muscle	stomach

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