Variant report

Variant	rs6574631
Chromosome Location	chr14:81675772-81675773
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	chr14:81671482..81674302-chr14:81674927..81677251,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10149681	0.87[CHD][hapmap]
rs1035948	0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11159493	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11159494	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11622105	0.81[AFR][1000 genomes]
rs11625861	0.85[CEU][hapmap];0.83[MEX][hapmap]
rs11850714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12147118	0.86[CHB][hapmap];0.87[CHD][hapmap];0.81[ASN][1000 genomes]
rs12372876	0.84[MEX][hapmap]
rs12590764	0.86[EUR][1000 genomes]
rs1864167	0.89[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1864169	0.83[CHB][hapmap]
rs1885601	0.89[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1951614	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1951615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1957546	0.85[CHD][hapmap]
rs1957549	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1991516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2099108	0.82[ASN][1000 genomes]
rs2241621	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs2288497	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2288499	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2371570	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs3815953	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4363794	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55643303	0.93[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs55822231	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs56835982	0.88[AFR][1000 genomes]
rs61980899	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61980900	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7141288	0.90[AFR][1000 genomes]
rs7142641	0.83[CHB][hapmap];0.87[CHD][hapmap]
rs7148100	0.83[CHB][hapmap];0.87[CHD][hapmap]
rs7149672	0.87[CHB][hapmap];0.87[CHD][hapmap];0.81[ASN][1000 genomes]
rs7160569	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs759939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8004096	0.86[EUR][1000 genomes]
rs8007841	0.86[CHD][hapmap];0.80[ASN][1000 genomes]
rs8008870	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs8009519	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8011097	0.86[EUR][1000 genomes]
rs8014406	0.83[CHB][hapmap];0.87[CHD][hapmap]
rs8015423	0.89[ASW][hapmap];0.85[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.92[LWK][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs8016982	0.87[CHB][hapmap]
rs8019108	0.81[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap]
rs8021125	0.86[EUR][1000 genomes]
rs8021385	0.86[EUR][1000 genomes]
rs9646167	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9806020	0.86[CHD][hapmap]
rs9806027	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9944085	0.89[ASW][hapmap];0.81[CEU][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap]

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	nsv832841	chr14:81588322-81743921	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	86 gene(s)	inside rSNPs	diseases
2	nsv902117	chr14:81643800-81682392	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6574631	STON2	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:81637000-81683800	Weak transcription	Small Intestine	intestine
2	chr14:81643800-81683200	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr14:81644200-81683600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr14:81644600-81685400	Weak transcription	Right Ventricle	heart
5	chr14:81649200-81677800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr14:81650600-81676600	Strong transcription	Placenta	Placenta
7	chr14:81651000-81685000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr14:81652600-81685400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr14:81654200-81683200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr14:81656600-81682800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr14:81656600-81683000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr14:81656600-81683400	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr14:81659400-81676600	Weak transcription	NHLF	lung
14	chr14:81660800-81685400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr14:81661000-81685400	Weak transcription	Aorta	Aorta
16	chr14:81662600-81684600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr14:81662800-81685400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr14:81663000-81683200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr14:81663000-81683800	Weak transcription	Fetal Brain Male	brain
20	chr14:81666400-81683400	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr14:81666800-81678600	Strong transcription	Dnd41	blood
22	chr14:81666800-81685000	Weak transcription	Stomach Mucosa	stomach
23	chr14:81667000-81682800	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr14:81667000-81682800	Strong transcription	Fetal Thymus	thymus
25	chr14:81667400-81678000	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr14:81667400-81683200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr14:81667600-81676400	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr14:81667600-81676600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr14:81667600-81676600	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr14:81667600-81678600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr14:81667600-81684000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr14:81667800-81678800	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr14:81667800-81682000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr14:81668000-81676800	Strong transcription	Primary T cells from cord blood	blood
35	chr14:81669200-81677400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr14:81669600-81684600	Weak transcription	HSMMtube	muscle
37	chr14:81669800-81677400	Weak transcription	A549	lung
38	chr14:81670400-81679200	Weak transcription	NHDF-Ad	bronchial
39	chr14:81670600-81685200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr14:81671200-81676400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr14:81671200-81683400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr14:81671400-81676400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr14:81671400-81679200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr14:81671600-81675800	Weak transcription	HMEC	breast
45	chr14:81671600-81676400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr14:81671600-81676600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr14:81671600-81678200	Strong transcription	Duodenum Mucosa	Duodenum
48	chr14:81671800-81676000	Weak transcription	Osteobl	bone
49	chr14:81672000-81675800	Strong transcription	Fetal Muscle Trunk	muscle
50	chr14:81672000-81677000	Strong transcription	Fetal Muscle Leg	muscle

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