Variant report

Variant	rs9285425
Chromosome Location	chr6:117871836-117871837
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:117870867..117873766-chr6:117883211..117885985,2	K562	blood:
2	chr6:117802413..117805335-chr6:117870908..117875397,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164465	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10457315	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10457318	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10872153	0.85[EUR][1000 genomes]
rs11153672	0.94[JPT][hapmap]
rs12205963	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1501474	0.85[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes]
rs1532680	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1759	0.84[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1967193	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1967194	0.82[EUR][1000 genomes]
rs2062663	0.85[CHB][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes]
rs2071825	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2088870	0.85[EUR][1000 genomes]
rs210617	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs210630	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs210633	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs210637	0.85[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs210639	0.84[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs210642	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3752848	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4946265	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4946267	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4946269	0.85[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4946273	0.84[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs67663020	0.81[EUR][1000 genomes]
rs9285426	0.85[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs9320612	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9320614	0.81[EUR][1000 genomes]
rs9320616	0.82[EUR][1000 genomes]
rs9320617	0.83[EUR][1000 genomes]
rs9374671	0.85[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9374674	0.83[EUR][1000 genomes]
rs9387491	0.85[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9401014	0.85[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9401019	0.82[EUR][1000 genomes]
rs9401023	0.82[EUR][1000 genomes]
rs9489223	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9489238	0.84[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes]
rs9767060	0.83[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532050	chr6:117528154-118203005	ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Height	23563607	GWAS catalog

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:117863400-117872200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:117868200-117872000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:117868600-117872400	Genic enhancers	NHEK	skin
4	chr6:117869400-117872200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
5	chr6:117869600-117872000	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr6:117869600-117872000	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr6:117869600-117872200	Enhancers	Placenta Amnion	Placenta Amnion
8	chr6:117869600-117872400	Enhancers	Fetal Thymus	thymus
9	chr6:117869800-117872000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:117869800-117872200	Enhancers	Fetal Lung	lung
11	chr6:117869800-117872400	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr6:117869800-117874200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:117869800-117880000	Weak transcription	Aorta	Aorta
14	chr6:117869800-117880000	Weak transcription	Brain Substantia Nigra	brain
15	chr6:117869800-117882600	Weak transcription	Brain Germinal Matrix	brain
16	chr6:117869800-117883200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:117869800-117884200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:117869800-117884400	Weak transcription	Ovary	ovary
19	chr6:117869800-117885200	Weak transcription	Fetal Stomach	stomach
20	chr6:117869800-117889000	Weak transcription	Left Ventricle	heart
21	chr6:117869800-117889400	Weak transcription	Psoas Muscle	Psoas
22	chr6:117869800-117889600	Weak transcription	Colonic Mucosa	Colon
23	chr6:117869800-117894400	Weak transcription	Lung	lung
24	chr6:117869800-117903800	Weak transcription	Spleen	Spleen
25	chr6:117869800-117904000	Weak transcription	Gastric	stomach
26	chr6:117869800-117904000	Weak transcription	Pancreas	Pancrea
27	chr6:117870000-117877000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr6:117870000-117879800	Weak transcription	Brain Hippocampus Middle	brain
29	chr6:117870000-117881600	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr6:117870000-117881800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr6:117870000-117882600	Weak transcription	Adipose Nuclei	Adipose
32	chr6:117870000-117884200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr6:117870000-117886800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr6:117870200-117876600	Weak transcription	Liver	Liver
35	chr6:117870200-117879400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr6:117870200-117884200	Weak transcription	Fetal Brain Male	brain
37	chr6:117870400-117872200	Enhancers	K562	blood
38	chr6:117870400-117874000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr6:117870400-117875000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr6:117870400-117876400	Weak transcription	NHLF	lung
41	chr6:117870400-117876600	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr6:117870400-117879800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr6:117870400-117880000	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr6:117870400-117880200	Weak transcription	Esophagus	oesophagus
45	chr6:117870400-117880400	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr6:117870400-117883000	Weak transcription	Placenta	Placenta
47	chr6:117870400-117883800	Weak transcription	Brain Angular Gyrus	brain
48	chr6:117870400-117883800	Weak transcription	Fetal Muscle Trunk	muscle
49	chr6:117870400-117884000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr6:117870400-117884000	Weak transcription	Stomach Smooth Muscle	stomach

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