Variant report

Variant	rs277952
Chromosome Location	chr5:70912681-70912682
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	chr5:70911415..70915310-chr5:70916318..70918922,4	MCF-7	breast:
2	chr5:70905852..70907544-chr5:70911927..70914158,2	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs157192	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs157193	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs166758	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs175871	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs277927	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs277935	0.86[EUR][1000 genomes]
rs277951	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277953	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs277955	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs277956	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs277975	0.86[CHB][hapmap]
rs277977	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs277982	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs277983	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs277984	0.88[ASN][1000 genomes]
rs277987	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs277988	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs277989	0.86[ASN][1000 genomes]
rs277990	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs277991	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs277992	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs277993	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs277994	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277998	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs282357	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs368462	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs412766	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs457539	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4703617	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034703	chr5:70391173-70995695	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats 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	28 gene(s)	inside rSNPs	diseases
2	nsv830340	chr5:70797113-70967110	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs277952	FOXD1	cis	cerebellum	SCAN
rs277952	GFM2	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:70883800-70916400	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr5:70884800-70934800	Weak transcription	Fetal Brain Male	brain
3	chr5:70893400-70916600	Weak transcription	Gastric	stomach
4	chr5:70893600-70930200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr5:70894000-70916400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr5:70895800-70937800	Weak transcription	Colonic Mucosa	Colon
7	chr5:70897000-70925800	Weak transcription	Right Ventricle	heart
8	chr5:70897200-70916600	Weak transcription	Esophagus	oesophagus
9	chr5:70897200-70930000	Weak transcription	Psoas Muscle	Psoas
10	chr5:70897400-70921000	Weak transcription	Fetal Heart	heart
11	chr5:70897400-70933800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr5:70897800-70916400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr5:70897800-70944800	Weak transcription	Small Intestine	intestine
14	chr5:70898200-70944200	Weak transcription	Osteobl	bone
15	chr5:70898400-70935400	Weak transcription	NHDF-Ad	bronchial
16	chr5:70898400-70955000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr5:70898600-70915800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr5:70898600-70922400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr5:70898600-70948400	Weak transcription	Brain Germinal Matrix	brain
20	chr5:70900000-70944800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr5:70900200-70916600	Weak transcription	Hela-S3	cervix
22	chr5:70900200-70925800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:70900200-70928200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr5:70900200-70930800	Weak transcription	HMEC	breast
25	chr5:70900200-70945200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr5:70900400-70916400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr5:70900400-70916400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr5:70900400-70916400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr5:70900400-70922800	Weak transcription	Fetal Kidney	kidney
30	chr5:70900400-70927000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr5:70900400-70927600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr5:70900400-70927800	Weak transcription	Brain Substantia Nigra	brain
33	chr5:70900400-70931000	Weak transcription	K562	blood
34	chr5:70900400-70933200	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr5:70905800-70912800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr5:70905800-70913800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr5:70905800-70920200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr5:70906400-70919600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr5:70906600-70912800	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr5:70906600-70913200	Strong transcription	Fetal Intestine Small	intestine
41	chr5:70906600-70923400	Strong transcription	Primary T cells from cord blood	blood
42	chr5:70906600-70952400	Weak transcription	Stomach Mucosa	stomach
43	chr5:70906800-70912800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr5:70906800-70912800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr5:70906800-70914200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr5:70906800-70915000	Strong transcription	Primary B cells from cord blood	blood
47	chr5:70906800-70923400	Strong transcription	Liver	Liver
48	chr5:70907000-70912800	Strong transcription	Stomach Smooth Muscle	stomach
49	chr5:70907200-70913200	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr5:70907200-70914000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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