Variant report

Variant	rs553947
Chromosome Location	chr19:56139679-56139680
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:55897294..55899219-chr19:56138033..56139795,2	MCF-7	breast:
2	chr19:56134111..56137190-chr19:56138042..56141707,3	K562	blood:
3	chr19:56137436..56140208-chr19:56143830..56146164,3	MCF-7	breast:
4	chr19:56137710..56141334-chr19:56143393..56147099,4	K562	blood:
5	chr19:56134111..56136553-chr19:56137529..56140208,2	K562	blood:

Variant related genes	Relation type
ENSG00000108107	Chromatin interaction
ENSG00000213015	Chromatin interaction
ENSG00000171425	Chromatin interaction
ENSG00000179922	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs2459748	0.87[EUR][1000 genomes]
rs310464	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs310465	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs310467	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs310470	1.00[ASN][1000 genomes]
rs310471	1.00[ASN][1000 genomes]
rs504003	1.00[CHB][hapmap]
rs507498	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs520125	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs522669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs60193103	0.83[AFR][1000 genomes]
rs612211	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs636466	1.00[ASN][1000 genomes]
rs636467	1.00[ASN][1000 genomes]
rs637788	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[YRI][hapmap]
rs644230	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs681433	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7246799	1.00[ASN][1000 genomes]
rs7251872	0.86[ASN][1000 genomes]
rs7257611	0.87[EUR][1000 genomes]
rs889091	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912473	chr19:55874642-56145428	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
2	nsv912486	chr19:55977909-56145428	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv912487	chr19:55977909-56215184	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv912494	chr19:56026072-56215184	Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
5	nsv912496	chr19:56040051-56145428	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
6	nsv912497	chr19:56041848-56145428	Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	nsv912498	chr19:56041848-56215184	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
8	nsv828643	chr19:56059280-56154823	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
9	nsv912500	chr19:56078722-56175515	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
10	nsv912501	chr19:56093365-56215184	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
11	nsv428026	chr19:56130849-56423514	Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	82 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56136400-56145600	Weak transcription	Right Atrium	heart
2	chr19:56136400-56146200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:56136600-56143000	Weak transcription	Stomach Mucosa	stomach
4	chr19:56136600-56143200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr19:56136800-56143000	Weak transcription	HepG2	liver
6	chr19:56136800-56143200	Weak transcription	Fetal Heart	heart
7	chr19:56136800-56143200	Weak transcription	Fetal Intestine Large	intestine
8	chr19:56136800-56143200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr19:56136800-56143600	Weak transcription	Colonic Mucosa	Colon
10	chr19:56136800-56144000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr19:56136800-56144000	Weak transcription	NHDF-Ad	bronchial
12	chr19:56136800-56145200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr19:56136800-56145200	Weak transcription	Fetal Muscle Leg	muscle
14	chr19:56136800-56145600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr19:56137000-56144000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr19:56137200-56145800	Weak transcription	Fetal Brain Female	brain
17	chr19:56138200-56143400	Weak transcription	Fetal Intestine Small	intestine
18	chr19:56138400-56143000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr19:56138400-56143200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr19:56138600-56143000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr19:56138600-56143000	Weak transcription	GM12878-XiMat	blood
22	chr19:56138800-56142800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr19:56138800-56142800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr19:56138800-56142800	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr19:56138800-56142800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr19:56138800-56143000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr19:56138800-56143000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr19:56138800-56143000	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr19:56138800-56143000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr19:56138800-56143000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr19:56138800-56145600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr19:56139200-56142800	Weak transcription	Primary T cells from cord blood	blood

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