Variant report

Variant	rs62120393
Chromosome Location	chr19:18335818-18335819
allele	A/G
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	JUND	chr19:18335800-18335956	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr19:18334536-18335973	K562	blood:	n/a	n/a
3	ZBTB7A	chr19:18335464-18336272	K562	blood:	n/a	chr19:18335733-18335744 chr19:18335592-18335599
4	CBX3	chr19:18335493-18336284	K562	blood:	n/a	n/a
5	CEBPB	chr19:18335468-18335823	K562	blood:	n/a	chr19:18335647-18335658
6	HDAC2	chr19:18335630-18336064	K562	blood:	n/a	n/a
7	YY1	chr19:18335320-18335847	HepG2	liver:	n/a	n/a
8	ZBTB7A	chr19:18335412-18336129	K562	blood:	n/a	chr19:18335733-18335744 chr19:18335592-18335599
9	E2F6	chr19:18335780-18336245	K562	blood:	n/a	chr19:18336070-18336080
10	MAZ	chr19:18335460-18335872	HepG2	liver:	n/a	n/a
11	ZMIZ1	chr19:18335737-18335936	K562	blood:	n/a	n/a
12	MAX	chr19:18334317-18336276	K562	blood:	n/a	chr19:18334579-18334595
13	BACH1	chr19:18335479-18335839	H1-hESC	embryonic stem cell:	n/a	n/a
14	NR2F2	chr19:18334510-18335927	MCF-7	breast:	n/a	chr19:18335169-18335184 chr19:18334982-18334997
15	YY1	chr19:18335790-18336034	K562	blood:	n/a	chr19:18335883-18335894
16	NR2F2	chr19:18334414-18336324	K562	blood:	n/a	chr19:18335169-18335184 chr19:18334982-18334997
17	EGR1	chr19:18335485-18336138	K562	blood:	n/a	chr19:18335883-18335896 chr19:18335682-18335692
18	MAX	chr19:18335783-18336188	K562	blood:	n/a	n/a
19	HCFC1	chr19:18334562-18335851	Hela-S3	cervix:	n/a	n/a
20	NR2F2	chr19:18335507-18336095	K562	blood:	n/a	n/a
21	CTCF	chr19:18335680-18335830	K562	blood:	n/a	chr19:18335810-18335823
22	CHD2	chr19:18335626-18335826	K562	blood:	n/a	n/a
23	EP300	chr19:18335734-18335907	K562	blood:	n/a	n/a
24	SP1	chr19:18335474-18336141	K562	blood:	n/a	chr19:18335593-18335602 chr19:18335589-18335603 chr19:18335594-18335603 chr19:18335882-18335891 chr19:18335593-18335603 chr19:18335593-18335603 chr19:18335592-18335604 chr19:18335883-18335892 chr19:18335594-18335603 chr19:18335592-18335604 chr19:18335997-18336018
25	CCNT2	chr19:18334654-18336082	K562	blood:	n/a	chr19:18335593-18335602 chr19:18335738-18335747 chr19:18335680-18335700
26	MYBL2	chr19:18335426-18335879	HepG2	liver:	n/a	n/a
27	TBP	chr19:18335485-18335917	K562	blood:	n/a	n/a
28	MAZ	chr19:18334872-18337410	IMR90	lung:	n/a	chr19:18336667-18336677
29	HDAC2	chr19:18335534-18335988	K562	blood:	n/a	n/a
30	POLR2A	chr19:18334583-18336199	K562	blood:	n/a	n/a
31	TBL1XR1	chr19:18334732-18335979	K562	blood:	n/a	n/a
32	YY1	chr19:18335450-18336137	K562	blood:	n/a	chr19:18335883-18335894
33	ELF1	chr19:18335763-18336125	K562	blood:	n/a	n/a
34	MEF2A	chr19:18335746-18336111	K562	blood:	n/a	n/a
35	ZNF143	chr19:18335561-18336075	H1-hESC	embryonic stem cell:	n/a	chr19:18335634-18335652 chr19:18335958-18335968 chr19:18335839-18335857
36	HMGN3	chr19:18334673-18336105	K562	blood:	n/a	n/a
37	MAZ	chr19:18335430-18336070	K562	blood:	n/a	n/a
38	EGR1	chr19:18335465-18336126	K562	blood:	n/a	chr19:18335883-18335896 chr19:18335682-18335692
39	GABPA	chr19:18335510-18336021	K562	blood:	n/a	n/a
40	SP4	chr19:18334363-18335883	H1-hESC	embryonic stem cell:	n/a	chr19:18335590-18335606 chr19:18334863-18334874 chr19:18334778-18334794 chr19:18334716-18334732
41	ELF1	chr19:18334660-18336236	GM12878	blood:	n/a	chr19:18335071-18335080

No.	Distal block	Cell Line	Cell type
1	chr19:18131740..18134624-chr19:18334636..18336432,2	K562	blood:
2	chr19:18334213..18336941-chr19:18433304..18435159,2	MCF-7	breast:
3	chr19:18302080..18305763-chr19:18333769..18336252,4	K562	blood:
4	chr19:18333775..18336002-chr19:19042076..19044771,2	K562	blood:
5	chr19:18334858..18337739-chr19:18526520..18530329,6	K562	blood:
6	chr19:18334911..18338218-chr19:18340999..18344328,5	MCF-7	breast:
7	chr19:18263338..18265453-chr19:18334676..18336331,2	K562	blood:
8	chr19:18312530..18316975-chr19:18331566..18338113,9	K562	blood:
9	chr19:18334725..18337698-chr19:18389039..18394023,6	K562	blood:
10	chr19:18263543..18265261-chr19:18334680..18337167,2	MCF-7	breast:
11	chr19:18312530..18319182-chr19:18329520..18338113,19	K562	blood:
12	chr19:18334471..18336688-chr19:18451268..18453619,2	K562	blood:
13	chr19:18282901..18285514-chr19:18334924..18337003,2	K562	blood:
14	chr19:18332417..18336925-chr19:18388887..18394072,11	K562	blood:
15	chr19:18333703..18336599-chr19:18524425..18529905,5	K562	blood:
16	chr19:18263953..18266175-chr19:18334676..18337393,3	K562	blood:
17	chr19:18334018..18336391-chr19:18495614..18498582,2	K562	blood:
18	chr19:18331180..18333406-chr19:18334762..18337599,3	MCF-7	breast:
19	chr19:18207111..18209121-chr19:18333968..18336429,3	K562	blood:

Variant related genes	Relation type
PDE4C	TF binding region
ENSG00000267959	Chromatin interaction
ENSG00000268173	Chromatin interaction
ENSG00000130517	Chromatin interaction
ENSG00000105650	Chromatin interaction
ENSG00000130511	Chromatin interaction
ENSG00000264175	Chromatin interaction
ENSG00000254858	Chromatin interaction
ENSG00000105647	Chromatin interaction
ENSG00000099308	Chromatin interaction
ENSG00000130522	Chromatin interaction
ENSG00000268650	Chromatin interaction
ENSG00000268032	Chromatin interaction
ENSG00000130513	Chromatin interaction
ENSG00000216490	Chromatin interaction
ENSG00000051128	Chromatin interaction
ENSG00000105649	Chromatin interaction
ENSG00000130520	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1046565	0.94[EUR][1000 genomes]
rs11881258	0.90[EUR][1000 genomes]
rs12460619	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12461021	0.89[EUR][1000 genomes]
rs12462801	0.91[EUR][1000 genomes]
rs17683509	0.90[EUR][1000 genomes]
rs17683539	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2049050	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2229228	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3803919	0.91[EUR][1000 genomes]
rs4458132	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808768	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55650549	0.90[EUR][1000 genomes]
rs62120367	0.82[EUR][1000 genomes]
rs62120368	0.89[EUR][1000 genomes]
rs62120382	0.89[EUR][1000 genomes]
rs62120383	0.90[EUR][1000 genomes]
rs62120385	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62120388	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7245576	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246274	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7259695	0.85[EUR][1000 genomes]
rs8100626	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8104010	0.88[EUR][1000 genomes]
rs8109807	0.84[AMR][1000 genomes];0.92[EUR][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	nsv1055932	chr19:17923918-18369944	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv543923	chr19:17923918-18369944	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
3	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
4	esv1837595	chr19:18085428-18393682	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
5	nsv911245	chr19:18206681-18338101	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers 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	37 gene(s)	inside rSNPs	diseases
6	nsv833775	chr19:18213761-18390074	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv911248	chr19:18224729-18338101	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv911249	chr19:18224729-18375846	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv911250	chr19:18224729-18376522	Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv911251	chr19:18224729-18422364	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
11	nsv911252	chr19:18234588-18338101	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
12	nsv911253	chr19:18240127-18418044	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
13	nsv916325	chr19:18244780-18534927	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
14	nsv911256	chr19:18255359-18338101	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
15	nsv911260	chr19:18288069-18386798	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
16	nsv911264	chr19:18309365-18369644	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
17	nsv470131	chr19:18326222-18389135	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62120393	KIAA1683	cis	brain	BrainEAC

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18334600-18336000	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr19:18334600-18337200	Enhancers	Spleen	Spleen
3	chr19:18334800-18336000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr19:18334800-18336000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
5	chr19:18334800-18336000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
6	chr19:18334800-18336000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr19:18334800-18336000	Enhancers	Fetal Heart	heart
8	chr19:18334800-18336000	Flanking Active TSS	Gastric	stomach
9	chr19:18334800-18336400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
10	chr19:18334800-18336600	Active TSS	Left Ventricle	heart
11	chr19:18334800-18337000	Active TSS	H9 Cell Line	embryonic stem cell
12	chr19:18335000-18336000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
13	chr19:18335000-18336000	Flanking Active TSS	Primary hematopoietic stem cells	blood
14	chr19:18335000-18336000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr19:18335000-18336000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
16	chr19:18335000-18336000	Active TSS	Right Atrium	heart
17	chr19:18335000-18336000	Bivalent/Poised TSS	Thymus	Thymus
18	chr19:18335000-18336200	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
19	chr19:18335000-18336200	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
20	chr19:18335000-18336200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
21	chr19:18335000-18336800	Bivalent/Poised TSS	Fetal Brain Female	brain
22	chr19:18335000-18337200	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr19:18335200-18336000	Active TSS	Psoas Muscle	Psoas
24	chr19:18335200-18336200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
25	chr19:18335200-18336200	Active TSS	Brain Anterior Caudate	brain
26	chr19:18335400-18336000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
27	chr19:18335400-18336000	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
28	chr19:18335400-18336200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr19:18335400-18336200	Bivalent Enhancer	Fetal Thymus	thymus
30	chr19:18335400-18336200	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
31	chr19:18335400-18337200	Bivalent Enhancer	Fetal Lung	lung
32	chr19:18335600-18336000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr19:18335600-18336000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
34	chr19:18335600-18336000	Flanking Bivalent TSS/Enh	Primary T helper memory cells from peripheral blood 2	blood
35	chr19:18335600-18336000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr19:18335600-18336000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr19:18335600-18336000	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
38	chr19:18335600-18336000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
39	chr19:18335600-18336000	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
40	chr19:18335600-18336000	Bivalent/Poised TSS	Brain Substantia Nigra	brain
41	chr19:18335600-18336000	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
42	chr19:18335600-18336000	Flanking Bivalent TSS/Enh	Placenta	Placenta
43	chr19:18335600-18336000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
44	chr19:18335600-18336000	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
45	chr19:18335600-18336000	Flanking Active TSS	GM12878-XiMat	blood
46	chr19:18335600-18336000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
47	chr19:18335600-18336000	Flanking Active TSS	NHLF	lung
48	chr19:18335600-18336200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
49	chr19:18335600-18336200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
50	chr19:18335600-18336200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell

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