Variant report

Variant	rs52875
Chromosome Location	chr6:14884396-14884397
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:14883074..14885637-chr6:15431868..15434468,2	K562	blood:
2	chr6:14881565..14884528-chr6:15089043..15091614,2	MCF-7	breast:
3	chr6:14882657..14885190-chr6:14887791..14890499,2	K562	blood:
4	chr6:14882855..14884940-chr6:15106180..15108933,2	K562	blood:

Variant related genes	Relation type
ENSG00000234261	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10949261	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12190539	0.87[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.93[EUR][1000 genomes]
rs12374664	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1258993	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16875788	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16875810	0.88[EUR][1000 genomes]
rs2124291	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2168315	0.88[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes]
rs373633	1.00[CEU][hapmap];0.81[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs387877	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs389438	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs394849	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs403392	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs410494	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41472949	0.94[CEU][hapmap];0.90[JPT][hapmap]
rs423468	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs425233	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs443427	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62390307	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62390308	0.87[EUR][1000 genomes]
rs62390309	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62390310	0.87[EUR][1000 genomes]
rs62390312	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62390313	0.92[EUR][1000 genomes]
rs62390314	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62390316	0.89[EUR][1000 genomes]
rs62390318	0.92[EUR][1000 genomes]
rs62390319	0.92[EUR][1000 genomes]
rs62390320	0.88[EUR][1000 genomes]
rs62390321	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6912084	0.88[EUR][1000 genomes]
rs6912613	0.92[EUR][1000 genomes]
rs72826859	0.87[EUR][1000 genomes]
rs72826868	0.90[EUR][1000 genomes]
rs72826874	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72826878	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9476670	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9476671	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9476672	0.92[EUR][1000 genomes];0.88[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	nsv1031668	chr6:14774036-15044308	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv538138	chr6:14774036-15044308	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1017572	chr6:14830510-14906933	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:14871600-14886600	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr6:14877400-14889000	Weak transcription	Duodenum Mucosa	Duodenum
3	chr6:14878200-14885600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr6:14879200-14884400	Weak transcription	K562	blood
5	chr6:14880200-14884800	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr6:14880200-14884800	Enhancers	Adipose Nuclei	Adipose
7	chr6:14880400-14884800	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr6:14880400-14886400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:14880400-14886400	Enhancers	Fetal Stomach	stomach
10	chr6:14880600-14884800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:14880800-14889000	Weak transcription	Spleen	Spleen
12	chr6:14881000-14884400	Enhancers	NH-A	brain
13	chr6:14881000-14885000	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr6:14881200-14884600	Enhancers	Muscle Satellite Cultured Cells	--
15	chr6:14881200-14884800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:14881400-14884400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr6:14881600-14888800	Weak transcription	A549	lung
18	chr6:14881800-14884400	Enhancers	Right Ventricle	heart
19	chr6:14881800-14884800	Enhancers	H1 Cell Line	embryonic stem cell
20	chr6:14882000-14886600	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr6:14882200-14884800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr6:14882400-14884600	Enhancers	Psoas Muscle	Psoas
23	chr6:14882400-14884800	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr6:14882400-14884800	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr6:14882400-14884800	Enhancers	Fetal Muscle Leg	muscle
26	chr6:14882400-14885200	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr6:14882400-14885200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr6:14882600-14884600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr6:14882600-14884800	Enhancers	H9 Cell Line	embryonic stem cell
30	chr6:14882600-14884800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr6:14882600-14884800	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr6:14882600-14884800	Enhancers	Fetal Muscle Trunk	muscle
33	chr6:14882800-14884600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
34	chr6:14882800-14884800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr6:14882800-14884800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr6:14882800-14884800	Enhancers	Ovary	ovary
37	chr6:14883200-14884600	Enhancers	HSMMtube	muscle
38	chr6:14883200-14886200	Weak transcription	Lung	lung
39	chr6:14883200-14888400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:14883200-14888400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr6:14883200-14889200	Weak transcription	Small Intestine	intestine
42	chr6:14883400-14884400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:14883400-14884600	Weak transcription	Fetal Kidney	kidney
44	chr6:14883400-14885800	Weak transcription	Right Atrium	heart
45	chr6:14883600-14884600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr6:14883600-14884800	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr6:14883600-14889000	Weak transcription	Stomach Mucosa	stomach
48	chr6:14883800-14884600	Enhancers	Placenta	Placenta
49	chr6:14883800-14884800	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr6:14883800-14884800	Enhancers	Left Ventricle	heart

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