Variant report

Variant	rs2304169
Chromosome Location	chr19:19976701-19976702
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:337)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:337 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr19:19976584-19977158	NT2-D1	testis:	n/a	chr19:19976967-19976978 chr19:19976962-19976970 chr19:19976961-19976971 chr19:19976949-19976971
2	EBF1	chr19:19976696-19976896	GM12878	blood:	n/a	n/a
3	FOS	chr19:19976447-19976787	GM12878	blood:	n/a	chr19:19976563-19976572
4	MAZ	chr19:19976432-19977322	IMR90	lung:	n/a	n/a
5	HEY1	chr19:19976408-19977009	HepG2	liver:	n/a	n/a
6	TAF1	chr19:19976416-19977482	GM12878	blood:	n/a	n/a
7	RELA	chr19:19976568-19977079	GM15510	blood:	n/a	n/a
8	YY1	chr19:19976477-19977446	K562	blood:	n/a	chr19:19976967-19976978 chr19:19976556-19976567 chr19:19976962-19976970 chr19:19976961-19976971 chr19:19976949-19976971
9	BHLHE40	chr19:19976605-19977041	K562	blood:	n/a	n/a
10	IRF1	chr19:19976464-19976843	K562	blood:	n/a	chr19:19976563-19976577
11	USF1	chr19:19976545-19976808	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr19:19976491-19977191	MCF10A-Er-Src	breast:	n/a	n/a
13	NFIC	chr19:19976411-19976895	GM12878	blood:	n/a	n/a
14	RFX5	chr19:19976200-19977933	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr19:19976586-19976921	HepG2	liver:	n/a	n/a
16	TAF1	chr19:19976529-19977146	GM12891	blood:	n/a	n/a
17	USF2	chr19:19976460-19976859	GM12878	blood:	n/a	n/a
18	NFYA	chr19:19976472-19976763	Hela-S3	cervix:	n/a	chr19:19976582-19976596 chr19:19976584-19976594
19	GATA1	chr19:19976414-19976768	PBDE	blood:	n/a	n/a
20	REST	chr19:19976517-19977006	HepG2	liver:	n/a	n/a
21	TAF7	chr19:19976570-19977135	H1-hESC	embryonic stem cell:	n/a	n/a
22	MYBL2	chr19:19976413-19977034	HepG2	liver:	n/a	n/a
23	PML	chr19:19976494-19977000	K562	blood:	n/a	n/a
24	CEBPD	chr19:19976555-19976963	HepG2	liver:	n/a	n/a
25	POLR2A	chr19:19976449-19977645	GM12878	blood:	n/a	n/a
26	POLR2A	chr19:19976385-19977811	K562	blood:	n/a	n/a
27	HCFC1	chr19:19976586-19977094	K562	blood:	n/a	n/a
28	MAZ	chr19:19976475-19977320	GM12878	blood:	n/a	n/a
29	MYC	chr19:19976565-19976788	HepG2	liver:	n/a	chr19:19976639-19976649
30	POLR2A	chr19:19976416-19977416	H1-neurons	neurons:	n/a	n/a
31	TAF1	chr19:19976444-19977352	PFSK-1	brain:	n/a	n/a
32	TBP	chr19:19976472-19977809	K562	blood:	n/a	n/a
33	NR2F2	chr19:19976393-19977144	K562	blood:	n/a	n/a
34	POU2F2	chr19:19976437-19977179	GM12878	blood:	n/a	chr19:19976559-19976571
35	TAF1	chr19:19976645-19976878	SK-N-SH	brain:	n/a	n/a
36	NR2F2	chr19:19976514-19976922	K562	blood:	n/a	n/a
37	ELF1	chr19:19976477-19977237	GM12878	blood:	n/a	n/a
38	MAX	chr19:19976459-19976824	ECC-1	luminal epithelium:	n/a	chr19:19976639-19976649
39	USF1	chr19:19976473-19976865	SK-N-SH_RA	brain:	n/a	n/a
40	MAX	chr19:19976421-19977428	HepG2	liver:	n/a	chr19:19976639-19976649
41	YY1	chr19:19976466-19977998	GM12878	blood:	n/a	chr19:19976967-19976978 chr19:19976556-19976567 chr19:19976962-19976970 chr19:19976961-19976971 chr19:19976949-19976971
42	POLR2A	chr19:19976513-19977034	HUVEC	blood vessel:	n/a	n/a
43	SP2	chr19:19976415-19976759	H1-hESC	embryonic stem cell:	n/a	chr19:19976559-19976574
44	POLR2A	chr19:19976358-19978092	GM12892	blood:	n/a	n/a
45	ZNF384	chr19:19976661-19977525	K562	blood:	n/a	n/a
46	TAF1	chr19:19976494-19977128	MCF-7	breast:	n/a	n/a
47	GATA3	chr19:19976395-19976837	MCF-7	breast:	n/a	n/a
48	BRCA1	chr19:19976593-19976923	HepG2	liver:	n/a	n/a
49	MYC	chr19:19976568-19976776	MCF-7	breast:	n/a	chr19:19976639-19976649
50	SIN3AK20	chr19:19976528-19976894	HepG2	liver:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:19976679-19976729	SAEC	small airway:	n/a
2	chr19:19976679-19976729	AG04449	skin:	fetal
3	chr19:19976679-19976729	SKMC	muscle:	n/a
4	chr19:19976679-19976729	GM12878	blood:	n/a
5	chr19:19976679-19976729	BJ	skin:	n/a
6	chr19:19976679-19976729	HUVEC	blood vessel:	n/a
7	chr19:19976679-19976729	SK-N-SH	brain:	n/a
8	chr19:19976679-19976729	HEK293	kidney:	embryo
9	chr19:19976679-19976729	HepG2	liver:	n/a
10	chr19:19976679-19976729	PFSK-1	brain:	n/a
11	chr19:19976679-19976729	HCT-116	colon:	n/a
12	chr19:19976679-19976729	NHBE	bronchial:	n/a
13	chr19:19976679-19976729	GM19239	blood:	n/a
14	chr19:19976679-19976729	AoSMC	blood vessel:	n/a
15	chr19:19976679-19976729	A549	lung:	n/a
16	chr19:19976679-19976729	AG09319	gingival:	n/a
17	chr19:19976679-19976729	MCF-7	breast:	n/a
18	chr19:19976679-19976729	Jurkat	blood:	n/a
19	chr19:19976679-19976729	GM12892	blood:	n/a
20	chr19:19976679-19976729	HEEpiC	esophagus:	n/a
21	chr19:19976679-19976729	HNPCEpiC	eye:	n/a
22	chr19:19976679-19976729	SK-N-SH_RA	brain:	n/a
23	chr19:19976679-19976729	GM06990	blood:	n/a
24	chr19:19976679-19976729	ProgFib	skin:	n/a
25	chr19:19976679-19976729	NB4	blood:	n/a
26	chr19:19976679-19976729	HCPEpiC	choroid plexus:	n/a
27	chr19:19976679-19976729	HCF	heart:	n/a
28	chr19:19976679-19976729	AG04450	lung:	fetal
29	chr19:19976679-19976729	Hela-S3	cervix:	n/a
30	chr19:19976679-19976729	HRPEpiC	eye:	n/a
31	chr19:19976679-19976729	RPTEC	kidney:	n/a
32	chr19:19976679-19976729	CMK	blood:	n/a
33	chr19:19976679-19976729	HL-60	blood:	n/a
34	chr19:19976679-19976729	BE2_C	brain:	n/a
35	chr19:19976679-19976729	NT2-D1	testis:	n/a
36	chr19:19976679-19976729	LNCaP	prostate:	n/a
37	chr19:19976679-19976729	ECC-1	luminal epithelium:	n/a
38	chr19:19976679-19976729	K562	blood:	n/a
39	chr19:19976679-19976729	GM12891	blood:	n/a
40	chr19:19976679-19976729	NHDF-neo	bronchial:	n/a
41	chr19:19976679-19976729	SK-N-MC	brain:	n/a
42	chr19:19976679-19976729	HMEC	breast:	n/a
43	chr19:19976679-19976729	HRCEpiC	kidney:	n/a
44	chr19:19976679-19976729	HIPEpiC	eye:	n/a
45	chr19:19976679-19976729	HRE	kidney:	n/a
46	chr19:19976679-19976729	AG10803	skin:	n/a
47	chr19:19976679-19976729	PANC-1	pancreas:	n/a
48	chr19:19976679-19976729	AG09309	skin:	n/a
49	chr19:19976679-19976729	T-47D	breast:	n/a
50	chr19:19976679-19976729	HPAEpiC	pulmonary alveolar:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr19:19975991..19979508-chr19:19981059..19984923,4	K562	blood:
2	chr19:19976218..19978192-chr19:20011161..20013662,4	K562	blood:
3	chr19:19966687..19968532-chr19:19975349..19978266,2	MCF-7	breast:
4	chr19:19779650..19782100-chr19:19976513..19978467,2	MCF-7	breast:
5	chr19:19976692..19979119-chr19:20011140..20013486,2	K562	blood:

No data

Variant related genes	Relation type
ZNF253	TF binding region
ZNF253	CpG island
ENSG00000270270	Chromatin interaction
ENSG00000181896	Chromatin interaction
ENSG00000270325	Chromatin interaction
ENSG00000267268	Chromatin interaction
ENSG00000184635	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10415754	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10421280	0.83[AFR][1000 genomes]
rs1469700	0.83[AFR][1000 genomes]
rs1469701	0.81[AFR][1000 genomes]
rs1469702	0.81[AFR][1000 genomes]
rs2116888	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28888982	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3926422	0.81[AFR][1000 genomes]
rs4808221	0.87[AFR][1000 genomes]
rs4809002	0.87[AFR][1000 genomes]
rs4809003	0.87[AFR][1000 genomes]
rs66624169	0.87[AFR][1000 genomes]
rs7250258	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7252427	0.87[AFR][1000 genomes]
rs7260247	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv911314	chr19:19866371-20021046	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking 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	27 gene(s)	inside rSNPs	diseases
3	nsv519535	chr19:19871250-20595412	Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
4	nsv911315	chr19:19872093-20021046	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv911316	chr19:19890450-20021046	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription 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	20 gene(s)	inside rSNPs	diseases
6	nsv961192	chr19:19906394-20083740	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	esv3319016	chr19:19917475-20819154	Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
8	esv3319017	chr19:19917475-20819154	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
9	esv3413756	chr19:19936066-20072059	ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	esv3380276	chr19:19936583-20073601	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1066792	chr19:19940585-20000701	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	esv3429980	chr19:19943721-20102072	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv1061846	chr19:19946927-20595412	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
14	esv3390957	chr19:19965887-20819154	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
15	nsv869122	chr19:19969851-20595412	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
16	nsv1057569	chr19:19973268-20193556	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
17	nsv1059158	chr19:19973489-20576161	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2304169	ZNF253	cis	Nerve Tibial	GTEx
rs2304169	ZNF682	cis	Muscle Skeletal	GTEx
rs2304169	ZNF506	Cis_1M	lymphoblastoid	RTeQTL
rs2304169	ZNF253	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19975800-19978400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr19:19975800-19978400	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr19:19975800-19978800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr19:19976000-19976800	Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr19:19976000-19977200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:19976000-19977400	Active TSS	NHEK	skin
7	chr19:19976000-19977600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr19:19976000-19977600	Active TSS	Osteobl	bone
9	chr19:19976000-19978000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr19:19976000-19978200	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr19:19976000-19978200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr19:19976000-19978200	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr19:19976000-19978400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr19:19976000-19978400	Active TSS	Rectal Smooth Muscle	rectum
15	chr19:19976000-19978400	Active TSS	HMEC	breast
16	chr19:19976000-19978600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr19:19976000-19978600	Active TSS	Muscle Satellite Cultured Cells	--
18	chr19:19976000-19978600	Active TSS	Colon Smooth Muscle	Colon
19	chr19:19976000-19978800	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr19:19976000-19978800	Active TSS	Duodenum Mucosa	Duodenum
21	chr19:19976000-19979000	Active TSS	Brain Angular Gyrus	brain
22	chr19:19976000-19979200	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr19:19976000-19979200	Active TSS	Right Atrium	heart
24	chr19:19976200-19977000	Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr19:19976200-19977400	Active TSS	Primary hematopoietic stem cells	blood
26	chr19:19976200-19977600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr19:19976200-19977600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr19:19976200-19977600	Active TSS	Adipose Nuclei	Adipose
29	chr19:19976200-19977600	Active TSS	Monocytes-CD14+_RO01746	blood
30	chr19:19976200-19978000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr19:19976200-19978000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr19:19976200-19978200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr19:19976200-19978200	Active TSS	Brain Hippocampus Middle	brain
34	chr19:19976200-19978200	Active TSS	Brain Substantia Nigra	brain
35	chr19:19976200-19978200	Active TSS	Skeletal Muscle Male	skeletal muscle
36	chr19:19976200-19978600	Active TSS	H9 Cell Line	embryonic stem cell
37	chr19:19976200-19978600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr19:19976200-19978600	Active TSS	Fetal Stomach	stomach
39	chr19:19976200-19978600	Active TSS	Right Ventricle	heart
40	chr19:19976200-19979200	Active TSS	Brain Germinal Matrix	brain
41	chr19:19976200-19979200	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr19:19976200-19979200	Active TSS	Stomach Smooth Muscle	stomach
43	chr19:19976400-19977200	Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr19:19976400-19977400	Active TSS	Primary monocytes fromperipheralblood	blood
45	chr19:19976400-19977400	Active TSS	Primary T cells fromperipheralblood	blood
46	chr19:19976400-19977400	Active TSS	Fetal Muscle Trunk	muscle
47	chr19:19976400-19977600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr19:19976400-19977600	Active TSS	Primary B cells from cord blood	blood
49	chr19:19976400-19977600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
50	chr19:19976400-19977600	Active TSS	Thymus	Thymus

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