Variant report

Variant	rs11955549
Chromosome Location	chr5:178322740-178322741
allele	C/T
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	CEBPD	chr5:178322635-178322988	HepG2	liver:	n/a	n/a
2	TAF1	chr5:178322595-178323369	HepG2	liver:	n/a	n/a
3	ZBTB33	chr5:178322736-178322935	HepG2	liver:	n/a	n/a
4	TAF1	chr5:178322678-178323734	H1-neurons	neurons:	n/a	n/a
5	RAD21	chr5:178322641-178323322	H1-hESC	embryonic stem cell:	n/a	chr5:178323172-178323186
6	POLR2A	chr5:178322647-178322999	GM12878	blood:	n/a	n/a
7	CHD2	chr5:178322704-178323070	H1-hESC	embryonic stem cell:	n/a	chr5:178323053-178323063
8	POLR2A	chr5:178322640-178323319	HCT-116	colon:	n/a	n/a
9	TAF1	chr5:178322721-178323691	H1-neurons	neurons:	n/a	n/a
10	ZNF143	chr5:178322656-178323091	GM12878	blood:	n/a	chr5:178322885-178322903 chr5:178322894-178322903 chr5:178322892-178322901
11	YY1	chr5:178322660-178323058	SK-N-SH_RA	brain:	n/a	chr5:178322987-178323001 chr5:178322993-178323002
12	NR2F2	chr5:178322569-178323420	MCF-7	breast:	n/a	n/a
13	HDAC2	chr5:178322617-178323441	MCF-7	breast:	n/a	n/a
14	POLR2A	chr5:178322721-178322844	A549	lung:	n/a	n/a
15	JUND	chr5:178322726-178322928	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr5:178322662-178323415	Hela-S3	cervix:	n/a	n/a
17	REST	chr5:178322693-178323527	SK-N-SH	brain:	n/a	chr5:178323172-178323182 chr5:178323217-178323226
18	POLR2A	chr5:178322642-178323175	ECC-1	luminal epithelium:	n/a	n/a
19	POLR2A	chr5:178322617-178323142	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr5:178322635-178323024	A549	lung:	n/a	n/a
21	EBF1	chr5:178322671-178322909	GM12878	blood:	n/a	n/a
22	TCF12	chr5:178322650-178323158	ECC-1	luminal epithelium:	n/a	chr5:178322804-178322811
23	MAX	chr5:178322648-178323344	SK-N-SH	brain:	n/a	chr5:178322991-178323001
24	POLR2A	chr5:178322598-178323328	MCF10A-Er-Src	breast:	n/a	n/a
25	MAX	chr5:178322617-178323486	H1-hESC	embryonic stem cell:	n/a	chr5:178322991-178323001
26	MAX	chr5:178322620-178323645	ECC-1	luminal epithelium:	n/a	chr5:178322991-178323001
27	HEY1	chr5:178322638-178323210	HepG2	liver:	n/a	chr5:178323083-178323098
28	CEBPB	chr5:178322401-178322967	H1-hESC	embryonic stem cell:	n/a	chr5:178322475-178322486
29	FOS	chr5:178322654-178323015	MCF10A-Er-Src	breast:	n/a	n/a
30	MAX	chr5:178322620-178323290	HepG2	liver:	n/a	chr5:178322991-178323001
31	MAX	chr5:178322616-178323317	SK-N-SH	brain:	n/a	chr5:178322991-178323001
32	POLR2A	chr5:178322668-178323036	HepG2	liver:	n/a	n/a
33	POLR2A	chr5:178322521-178323212	PANC-1	pancreas:	n/a	n/a
34	POLR2A	chr5:178322419-178323068	HepG2	liver:	n/a	n/a
35	YY1	chr5:178322737-178323096	ECC-1	luminal epithelium:	n/a	chr5:178322987-178323001 chr5:178322993-178323002
36	POLR2A	chr5:178322723-178322827	GM12878	blood:	n/a	n/a
37	CREB1	chr5:178322632-178323156	H1-hESC	embryonic stem cell:	n/a	n/a
38	TAF1	chr5:178322616-178323651	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr5:178322465-178323666	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr5:178322606-178322992	HepG2	liver:	n/a	n/a
41	POLR2A	chr5:178322655-178323089	A549	lung:	n/a	n/a
42	CTCF	chr5:178322640-178322790	SK-N-SH_RA	brain:	n/a	chr5:178322776-178322789
43	POLR2A	chr5:178322711-178322913	A549	lung:	n/a	n/a
44	ZNF143	chr5:178322673-178323391	H1-hESC	embryonic stem cell:	n/a	chr5:178322885-178322903 chr5:178322894-178322903 chr5:178322892-178322901
45	TBP	chr5:178322736-178322931	Hela-S3	cervix:	n/a	n/a
46	MAX	chr5:178322624-178323567	MCF-7	breast:	n/a	chr5:178322991-178323001
47	YY1	chr5:178322702-178322978	HCT-116	colon:	n/a	n/a
48	MAX	chr5:178322670-178323141	Hela-S3	cervix:	n/a	chr5:178322991-178323001
49	POLR2A	chr5:178322512-178323136	Hela-S3	cervix:	n/a	n/a
50	YY1	chr5:178322641-178323002	ECC-1	luminal epithelium:	n/a	chr5:178322987-178323001 chr5:178322993-178323002

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:178322737-178322787	NB4	blood:	n/a
2	chr5:178322737-178322787	HRPEpiC	eye:	n/a
3	chr5:178322737-178322787	HAEpiC	amniotic membrane:	n/a
4	chr5:178322737-178322787	PANC-1	pancreas:	n/a
5	chr5:178322737-178322787	SKMC	muscle:	n/a
6	chr5:178322737-178322787	H1-hESC	embryonic stem cell:	embryo
7	chr5:178322737-178322787	MCF-7	breast:	n/a
8	chr5:178322737-178322787	SAEC	small airway:	n/a
9	chr5:178322737-178322787	HCF	heart:	n/a
10	chr5:178322737-178322787	GM12891	blood:	n/a
11	chr5:178322737-178322787	HNPCEpiC	eye:	n/a
12	chr5:178322737-178322787	GM12892	blood:	n/a
13	chr5:178322737-178322787	AG04450	lung:	fetal
14	chr5:178322737-178322787	HEEpiC	esophagus:	n/a
15	chr5:178322737-178322787	ECC-1	luminal epithelium:	n/a
16	chr5:178322737-178322787	SK-N-SH	brain:	n/a
17	chr5:178322737-178322787	AG10803	skin:	n/a
18	chr5:178322737-178322787	BE2_C	brain:	n/a
19	chr5:178322737-178322787	AG09319	gingival:	n/a
20	chr5:178322737-178322787	CMK	blood:	n/a
21	chr5:178322737-178322787	RPTEC	kidney:	n/a
22	chr5:178322737-178322787	T-47D	breast:	n/a
23	chr5:178322737-178322787	Hepatocyte	liver:	n/a
24	chr5:178322737-178322787	HPAEpiC	pulmonary alveolar:	n/a
25	chr5:178322737-178322787	HEK293	kidney:	embryo
26	chr5:178322737-178322787	IMR90	lung:	fetal
27	chr5:178322737-178322787	HUVEC	blood vessel:	n/a
28	chr5:178322737-178322787	NH-A	brain:	n/a
29	chr5:178322737-178322787	LNCaP	prostate:	n/a
30	chr5:178322737-178322787	SK-N-SH_RA	brain:	n/a
31	chr5:178322737-178322787	HCM	heart:	n/a
32	chr5:178322737-178322787	U87	brain:	n/a
33	chr5:178322737-178322787	GM06990	blood:	n/a
34	chr5:178322737-178322787	HRCEpiC	kidney:	n/a
35	chr5:178322737-178322787	Jurkat	blood:	n/a
36	chr5:178322737-178322787	NT2-D1	testis:	n/a
37	chr5:178322737-178322787	PFSK-1	brain:	n/a
38	chr5:178322737-178322787	Hela-S3	cervix:	n/a
39	chr5:178322737-178322787	AoSMC	blood vessel:	n/a
40	chr5:178322737-178322787	ovcar-3	ovarian:	n/a
41	chr5:178322737-178322787	A549	lung:	n/a
42	chr5:178322737-178322787	AG04449	skin:	fetal
43	chr5:178322737-178322787	Caco-2	colon:	n/a
44	chr5:178322737-178322787	ProgFib	skin:	n/a
45	chr5:178322737-178322787	NHDF-neo	bronchial:	n/a
46	chr5:178322737-178322787	HCT-116	colon:	n/a
47	chr5:178322737-178322787	AG09309	skin:	n/a
48	chr5:178322737-178322787	HIPEpiC	eye:	n/a
49	chr5:178322737-178322787	HepG2	liver:	n/a
50	chr5:178322737-178322787	HCPEpiC	choroid plexus:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:178285646..178289279-chr5:178321547..178324884,4	MCF-7	breast:
2	chr5:178322017..178324460-chr5:178337015..178339677,2	MCF-7	breast:

Variant related genes	Relation type
ZFP2	TF binding region
ZFP2	CpG island
ENSG00000178338	Chromatin interaction
ENSG00000213328	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1046724	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11249600	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11744810	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11745435	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11748636	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11749871	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11955491	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11956161	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12516516	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13166562	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13171869	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13182467	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13189231	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13189941	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1496948	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1566105	0.84[EUR][1000 genomes]
rs17652441	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1845939	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2047356	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34904538	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35245718	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35974815	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35984063	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6894647	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6897952	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7445002	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7448421	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7448445	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7722159	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7722441	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs953741	0.82[AMR][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	nsv883218	chr5:178219855-178349391	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178313600-178322800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr5:178314400-178325000	Weak transcription	Fetal Brain Male	brain
3	chr5:178317200-178322800	Weak transcription	Gastric	stomach
4	chr5:178317400-178323200	Weak transcription	Fetal Heart	heart
5	chr5:178322400-178322800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
6	chr5:178322400-178322800	Flanking Active TSS	Placenta	Placenta
7	chr5:178322400-178323200	Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr5:178322400-178323400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr5:178322400-178323600	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr5:178322400-178323600	Active TSS	Brain Germinal Matrix	brain
11	chr5:178322400-178323600	Active TSS	Brain Substantia Nigra	brain
12	chr5:178322400-178323600	Active TSS	Psoas Muscle	Psoas
13	chr5:178322400-178323600	Active TSS	Hela-S3	cervix
14	chr5:178322400-178323800	Active TSS	H9 Cell Line	embryonic stem cell
15	chr5:178322400-178323800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr5:178322400-178323800	Active TSS	Brain Anterior Caudate	brain
17	chr5:178322400-178323800	Active TSS	Brain Cingulate Gyrus	brain
18	chr5:178322400-178323800	Active TSS	Duodenum Mucosa	Duodenum
19	chr5:178322400-178323800	Active TSS	Fetal Intestine Large	intestine
20	chr5:178322400-178323800	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr5:178322400-178323800	Active TSS	Right Atrium	heart
22	chr5:178322400-178324000	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr5:178322400-178324000	Active TSS	Rectal Mucosa Donor 31	rectum
24	chr5:178322400-178324200	Active TSS	Fetal Brain Female	brain
25	chr5:178322600-178322800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
26	chr5:178322600-178322800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr5:178322600-178322800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
28	chr5:178322600-178322800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr5:178322600-178322800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr5:178322600-178322800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
31	chr5:178322600-178322800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr5:178322600-178322800	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
33	chr5:178322600-178322800	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr5:178322600-178322800	Flanking Active TSS	Fetal Muscle Leg	muscle
35	chr5:178322600-178322800	Flanking Active TSS	Ovary	ovary
36	chr5:178322600-178322800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr5:178322600-178322800	Flanking Active TSS	Stomach Smooth Muscle	stomach
38	chr5:178322600-178323000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr5:178322600-178323000	Flanking Active TSS	Primary B cells from peripheral blood	blood
40	chr5:178322600-178323000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr5:178322600-178323200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr5:178322600-178323200	Active TSS	Primary B cells from cord blood	blood
43	chr5:178322600-178323200	Active TSS	Primary hematopoietic stem cells	blood
44	chr5:178322600-178323200	Active TSS	Cortex derived primary cultured neurospheres	brain
45	chr5:178322600-178323200	Active TSS	Fetal Muscle Trunk	muscle
46	chr5:178322600-178323200	ZNF genes & repeats	Spleen	Spleen
47	chr5:178322600-178323200	Active TSS	Dnd41	blood
48	chr5:178322600-178323200	Active TSS	NHEK	skin
49	chr5:178322600-178323400	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
50	chr5:178322600-178323400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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