Variant report

Variant	rs7025577
Chromosome Location	chr9:117661665-117661666
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:117659568..117662536-chr9:117667322..117669249,2	K562	blood:
2	chr9:117660650..117663296-chr9:117774626..117776386,2	MCF-7	breast:
3	chr9:117660259..117663236-chr9:117664218..117666178,2	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1006025	0.81[EUR][1000 genomes]
rs1006026	0.93[EUR][1000 genomes]
rs1006027	0.81[EUR][1000 genomes]
rs10081728	0.83[EUR][1000 genomes]
rs10817679	0.88[ASN][1000 genomes]
rs10817682	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10817683	0.93[EUR][1000 genomes]
rs10982445	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10982449	0.81[EUR][1000 genomes]
rs10982450	0.82[EUR][1000 genomes]
rs10982451	0.82[EUR][1000 genomes]
rs10982453	0.81[EUR][1000 genomes]
rs10982454	0.81[EUR][1000 genomes]
rs10982455	0.81[EUR][1000 genomes]
rs10982456	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1126711	0.96[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12337739	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12338765	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12347977	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12352646	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1322054	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1322056	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1322058	0.81[EUR][1000 genomes]
rs1322060	0.85[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs1322067	0.98[EUR][1000 genomes]
rs1407309	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17292087	0.84[EUR][1000 genomes]
rs2075533	0.91[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2181036	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2208640	0.83[EUR][1000 genomes]
rs2295800	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2418324	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2418325	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2974	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3181195	0.80[GIH][hapmap];0.84[EUR][1000 genomes]
rs3181197	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3181200	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3181201	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3181202	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3181348	0.91[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3181363	0.82[EUR][1000 genomes]
rs3181364	0.83[EUR][1000 genomes]
rs3181365	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3181366	0.83[EUR][1000 genomes]
rs3181367	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3181368	0.82[EUR][1000 genomes]
rs3181369	0.80[GIH][hapmap];0.82[EUR][1000 genomes]
rs3181370	0.82[EUR][1000 genomes]
rs3181371	0.82[EUR][1000 genomes]
rs3181372	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3181374	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3789879	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4978611	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4979470	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4979471	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4979472	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4979473	0.84[EUR][1000 genomes]
rs6478117	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7028578	0.82[EUR][1000 genomes]
rs7030090	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7032773	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7036962	0.81[EUR][1000 genomes]
rs7037640	0.82[EUR][1000 genomes]
rs726657	0.88[CEU][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs7858603	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7872878	0.94[EUR][1000 genomes]
rs911603	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs927373	0.82[EUR][1000 genomes]
rs927374	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs927375	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[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	nsv831695	chr9:117567626-117726247	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv893767	chr9:117627569-117689838	Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7025577	KIAA1958	cis	parietal	SCAN
rs7025577	ASTN2	cis	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117652600-117662000	Weak transcription	Gastric	stomach
2	chr9:117655200-117661800	Enhancers	Primary T killer memory cells from peripheral blood	blood
3	chr9:117655600-117664800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr9:117656200-117663400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr9:117656400-117663600	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr9:117657200-117662800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr9:117657200-117663600	Weak transcription	HSMMtube	muscle
8	chr9:117657600-117661800	Weak transcription	Stomach Mucosa	stomach
9	chr9:117657800-117661800	Weak transcription	Fetal Muscle Leg	muscle
10	chr9:117657800-117661800	Weak transcription	Right Ventricle	heart
11	chr9:117657800-117663200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr9:117657800-117664600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr9:117657800-117665400	Enhancers	HUVEC	blood vessel
14	chr9:117657800-117669600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr9:117658000-117662200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr9:117658000-117663200	Weak transcription	HMEC	breast
17	chr9:117658000-117663600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr9:117658200-117661800	Weak transcription	Placenta	Placenta
19	chr9:117658200-117663600	Weak transcription	Hela-S3	cervix
20	chr9:117658200-117663600	Weak transcription	NHEK	skin
21	chr9:117658200-117664600	Weak transcription	Duodenum Mucosa	Duodenum
22	chr9:117658400-117661800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr9:117658400-117663400	Weak transcription	A549	lung
24	chr9:117658400-117665200	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr9:117658400-117665800	Enhancers	NHDF-Ad	bronchial
26	chr9:117658400-117667400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr9:117658600-117661800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr9:117658600-117669200	Weak transcription	Fetal Stomach	stomach
29	chr9:117659200-117663400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr9:117659400-117663000	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr9:117659600-117662800	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr9:117659600-117663200	Enhancers	Primary B cells from peripheral blood	blood
33	chr9:117659600-117665400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr9:117659800-117662000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr9:117659800-117663400	Enhancers	Fetal Thymus	thymus
36	chr9:117660000-117662600	Enhancers	Primary hematopoietic stem cells	blood
37	chr9:117660000-117662800	Weak transcription	NH-A	brain
38	chr9:117660000-117663400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr9:117660200-117661800	Weak transcription	HSMM	muscle
40	chr9:117660200-117661800	Weak transcription	NHLF	lung
41	chr9:117660400-117663000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr9:117660600-117662800	Enhancers	Adipose Nuclei	Adipose
43	chr9:117660600-117665400	Enhancers	Osteobl	bone
44	chr9:117660600-117665600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr9:117660800-117661800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr9:117660800-117662000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr9:117660800-117662000	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr9:117661000-117661800	Enhancers	Rectal Mucosa Donor 29	rectum
49	chr9:117661000-117662000	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr9:117661000-117662600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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