Variant report

Variant	rs234342
Chromosome Location	chr19:40486171-40486172
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	POLR2A	chr19:40486022-40486305	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr19:40486026-40486209	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:40486155-40486435	K562	blood:	n/a	n/a
4	POLR2A	chr19:40486064-40486193	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr19:40486134-40486249	MCF-7	breast:	n/a	n/a
6	POLR2A	chr19:40485552-40486714	Hela-S3	cervix:	n/a	n/a
7	EP300	chr19:40485853-40487029	SK-N-SH	brain:	n/a	chr19:40486740-40486754
8	POLR2A	chr19:40485907-40486774	HepG2	liver:	n/a	n/a
9	POLR2A	chr19:40485733-40486395	HepG2	liver:	n/a	n/a
10	POLR2A	chr19:40486032-40486304	H1-neurons	neurons:	n/a	n/a
11	POLR2A	chr19:40485538-40486741	K562	blood:	n/a	n/a
12	POLR2A	chr19:40485549-40486879	K562	blood:	n/a	n/a
13	POLR2A	chr19:40485648-40486686	SK-N-MC	brain:	n/a	n/a
14	POLR2A	chr19:40472172-40495393	PANC-1	pancreas:	n/a	n/a
15	POLR2A	chr19:40485691-40486827	GM12878	blood:	n/a	n/a
16	POLR2A	chr19:40485787-40487655	PFSK-1	brain:	n/a	n/a
17	POLR2A	chr19:40485738-40486910	K562	blood:	n/a	n/a
18	POLR2A	chr19:40486062-40486206	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr19:40485500-40486814	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:40473089..40482317-chr19:40483091..40492558,21	K562	blood:
2	chr19:40475779..40479202-chr19:40484390..40487184,3	MCF-7	breast:

Variant related genes	Relation type
ZNF546	TF binding region
ENSG00000013275	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10410695	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10418448	1.00[EUR][1000 genomes]
rs10419218	1.00[EUR][1000 genomes]
rs10420514	1.00[EUR][1000 genomes]
rs10420687	1.00[EUR][1000 genomes]
rs10421243	1.00[EUR][1000 genomes]
rs10423298	1.00[EUR][1000 genomes]
rs10423800	1.00[EUR][1000 genomes]
rs10427117	1.00[EUR][1000 genomes]
rs11883159	1.00[EUR][1000 genomes]
rs13382054	1.00[EUR][1000 genomes]
rs170898	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs234297	1.00[EUR][1000 genomes]
rs234307	1.00[EUR][1000 genomes]
rs234312	1.00[EUR][1000 genomes]
rs234316	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs234319	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs234321	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs234322	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs234327	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs234339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2542302	1.00[EUR][1000 genomes]
rs2542311	1.00[AMR][1000 genomes]
rs28589691	0.93[AMR][1000 genomes]
rs28661993	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28776318	1.00[EUR][1000 genomes]
rs28832070	1.00[EUR][1000 genomes]
rs337795	1.00[EUR][1000 genomes]
rs57342065	1.00[EUR][1000 genomes]
rs58348431	1.00[EUR][1000 genomes]
rs59707868	1.00[EUR][1000 genomes]
rs60631264	1.00[EUR][1000 genomes]
rs61424085	1.00[EUR][1000 genomes]
rs7245930	1.00[EUR][1000 genomes]
rs7250945	1.00[EUR][1000 genomes]
rs7257627	1.00[EUR][1000 genomes]
rs7258111	1.00[EUR][1000 genomes]
rs73930675	1.00[EUR][1000 genomes]
rs73930678	1.00[EUR][1000 genomes]
rs73930679	1.00[EUR][1000 genomes]
rs8111518	1.00[EUR][1000 genomes]
rs8111741	1.00[EUR][1000 genomes]
rs9630860	1.00[EUR][1000 genomes]
rs9630868	1.00[EUR][1000 genomes]
rs9783944	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758498	chr19:40227904-40521130	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv2758760	chr19:40227904-40521130	Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv428022	chr19:40227904-40521130	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv917321	chr19:40403192-40694875	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent Enhancer 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	43 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40477800-40501800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:40478200-40488200	Strong transcription	Thymus	Thymus
3	chr19:40478200-40488400	Strong transcription	Fetal Stomach	stomach
4	chr19:40478200-40489200	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr19:40478200-40489200	Strong transcription	Primary B cells from cord blood	blood
6	chr19:40478200-40489400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr19:40478200-40489400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr19:40478200-40489600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr19:40478400-40488000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:40478400-40488200	Strong transcription	Fetal Muscle Trunk	muscle
11	chr19:40478400-40488200	Strong transcription	Fetal Muscle Leg	muscle
12	chr19:40478400-40488400	Strong transcription	Brain Anterior Caudate	brain
13	chr19:40478400-40488800	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr19:40478400-40488800	Strong transcription	Adipose Nuclei	Adipose
15	chr19:40478400-40489000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr19:40478400-40489000	Strong transcription	NH-A	brain
17	chr19:40478400-40489200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr19:40478400-40489200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr19:40478400-40489200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr19:40478400-40489400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr19:40478400-40489400	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr19:40478400-40489400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr19:40478400-40489400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr19:40478400-40490000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr19:40478400-40490400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr19:40478400-40491000	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr19:40478400-40491200	Weak transcription	Fetal Heart	heart
28	chr19:40478600-40488400	Strong transcription	Left Ventricle	heart
29	chr19:40478600-40488800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr19:40478600-40489200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr19:40478600-40489200	Strong transcription	Fetal Intestine Small	intestine
32	chr19:40478600-40489600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr19:40478600-40489600	Strong transcription	Liver	Liver
34	chr19:40478600-40489600	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr19:40478600-40489800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr19:40478600-40490000	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr19:40478600-40501800	Weak transcription	Right Atrium	heart
38	chr19:40479000-40488400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr19:40479000-40490200	Strong transcription	HSMMtube	muscle
40	chr19:40479200-40488400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr19:40479200-40490200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr19:40479600-40490200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr19:40480400-40489600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr19:40480800-40488200	Strong transcription	Gastric	stomach
45	chr19:40481200-40488200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr19:40481800-40487000	Weak transcription	Fetal Brain Male	brain
47	chr19:40481800-40489400	Weak transcription	Fetal Kidney	kidney
48	chr19:40481800-40490800	Weak transcription	Stomach Mucosa	stomach
49	chr19:40482600-40488000	Strong transcription	HepG2	liver
50	chr19:40482600-40488800	Strong transcription	Rectal Smooth Muscle	rectum

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