Variant report

Variant	rs56233820
Chromosome Location	chr12:120314304-120314305
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:120313416..120316416-chr17:41464359..41467641,4	K562	blood:
2	chr12:120313415..120316416-chr17:41464359..41467641,4	K562	blood:
3	chr12:120313396..120316395-chr17:41464679..41467181,3	MCF-7	breast:
4	chr12:120306038..120308979-chr12:120311898..120314369,2	MCF-7	breast:
5	chr12:120313729..120318058-chr12:120425281..120428238,3	K562	blood:

Variant related genes	Relation type
ENSG00000188825	Chromatin interaction
ENSG00000135127	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11064946	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12164852	0.91[AMR][1000 genomes]
rs12303725	0.95[EUR][1000 genomes]
rs12303871	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12307282	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12310524	0.83[AMR][1000 genomes]
rs12312594	1.00[AMR][1000 genomes]
rs12313808	1.00[AMR][1000 genomes]
rs12316230	0.91[AMR][1000 genomes]
rs12317711	0.91[AMR][1000 genomes]
rs12319537	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12319916	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12320276	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13313223	0.90[EUR][1000 genomes]
rs55906258	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56903823	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57243313	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57459050	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57487797	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57626094	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57908788	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58111169	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58399872	0.91[AMR][1000 genomes]
rs58893111	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59347602	0.95[EUR][1000 genomes]
rs59442639	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60392056	0.84[EUR][1000 genomes]
rs60588068	0.83[AMR][1000 genomes]
rs61507048	0.83[AMR][1000 genomes]
rs7304029	0.95[EUR][1000 genomes]
rs73418594	0.90[EUR][1000 genomes]
rs73420604	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73420611	0.83[AMR][1000 genomes]
rs73420615	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73420618	0.91[AMR][1000 genomes]
rs7967407	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv455727	chr12:120259679-120420670	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv560397	chr12:120259679-120420670	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv510575	chr12:120303163-120437490	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120223000-120314400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr12:120254800-120314600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:120277000-120314400	Weak transcription	Spleen	Spleen
4	chr12:120277200-120314600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr12:120279800-120314400	Weak transcription	Primary B cells from cord blood	blood
6	chr12:120286000-120314400	Weak transcription	Placenta	Placenta
7	chr12:120303000-120314400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr12:120305600-120314400	Weak transcription	Fetal Brain Male	brain
9	chr12:120305800-120314400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:120306600-120314400	Weak transcription	Fetal Intestine Large	intestine
11	chr12:120308200-120314400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:120313200-120314400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr12:120313600-120314400	Weak transcription	Small Intestine	intestine
14	chr12:120313800-120314400	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr12:120313800-120314400	Flanking Active TSS	GM12878-XiMat	blood
16	chr12:120313800-120314400	Flanking Active TSS	NHDF-Ad	bronchial
17	chr12:120313800-120314600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr12:120313800-120314600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr12:120313800-120314600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr12:120313800-120314600	Flanking Active TSS	Brain Germinal Matrix	brain
21	chr12:120313800-120314600	Flanking Active TSS	Dnd41	blood
22	chr12:120313800-120314600	Flanking Active TSS	Hela-S3	cervix
23	chr12:120314000-120314400	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr12:120314000-120314400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr12:120314000-120314400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr12:120314000-120314400	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr12:120314000-120314400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr12:120314000-120314400	Enhancers	Brain Substantia Nigra	brain
29	chr12:120314000-120314400	Flanking Active TSS	NHLF	lung
30	chr12:120314000-120314600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr12:120314000-120314600	Flanking Active TSS	A549	lung
32	chr12:120314000-120314600	Flanking Active TSS	HMEC	breast
33	chr12:120314000-120314600	Flanking Active TSS	HUVEC	blood vessel
34	chr12:120314000-120314600	Flanking Active TSS	K562	blood
35	chr12:120314000-120314800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr12:120314000-120314800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
37	chr12:120314000-120315400	Active TSS	Muscle Satellite Cultured Cells	--
38	chr12:120314000-120315400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr12:120314000-120315400	Active TSS	NH-A	brain
40	chr12:120314000-120315600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr12:120314000-120315600	Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr12:120314000-120315600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr12:120314000-120315800	Active TSS	H1 Cell Line	embryonic stem cell
44	chr12:120314000-120315800	Active TSS	H9 Cell Line	embryonic stem cell
45	chr12:120314000-120315800	Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr12:120314200-120314400	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
47	chr12:120314200-120314400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr12:120314200-120314400	Enhancers	Primary B cells from peripheral blood	blood
49	chr12:120314200-120314400	Active TSS	Primary T cells from cord blood	blood
50	chr12:120314200-120314400	Enhancers	Primary T cells fromperipheralblood	blood

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