Variant report

Variant	rs12700754
Chromosome Location	chr7:26754389-26754390
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10227140	0.83[CEU][hapmap]
rs10231161	0.81[CEU][hapmap]
rs1024454	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10256799	0.83[CEU][hapmap]
rs10261915	0.82[CEU][hapmap]
rs10807834	0.81[EUR][1000 genomes]
rs10951145	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs10951149	0.83[CEU][hapmap]
rs1123157	0.83[CEU][hapmap]
rs1123158	0.85[CEU][hapmap]
rs11764558	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11770043	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs11770344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11773029	0.85[CEU][hapmap]
rs12668948	0.82[EUR][1000 genomes]
rs12700755	0.83[CEU][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12700756	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12700757	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12700758	0.93[CEU][hapmap];0.80[EUR][1000 genomes]
rs12700759	0.82[CEU][hapmap]
rs12700761	0.85[CEU][hapmap]
rs12700762	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13186	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs1548022	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1548478	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs1548479	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs1548480	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1859101	0.82[CEU][hapmap]
rs2023819	0.83[CEU][hapmap]
rs2023821	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs212837	0.86[ASN][1000 genomes]
rs212842	0.85[CEU][hapmap]
rs212844	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs212845	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs212846	0.81[EUR][1000 genomes]
rs212847	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs212851	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs212852	0.81[CEU][hapmap]
rs212853	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs212854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs212855	0.80[EUR][1000 genomes]
rs212858	0.81[CEU][hapmap]
rs2237328	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs2282906	0.85[CEU][hapmap];0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2299101	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2299102	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs2391359	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs2391360	0.85[CEU][hapmap]
rs2893256	0.82[ASN][1000 genomes]
rs3801839	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs3801853	0.83[CEU][hapmap]
rs3801860	0.83[CEU][hapmap]
rs3801872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4719879	0.81[EUR][1000 genomes]
rs4722628	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4722631	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs4722632	0.93[ASN][1000 genomes]
rs4722637	0.84[ASN][1000 genomes]
rs496173	0.86[JPT][hapmap]
rs498561	0.84[JPT][hapmap]
rs5012512	0.81[CEU][hapmap]
rs58988613	0.81[EUR][1000 genomes]
rs601106	0.86[JPT][hapmap]
rs6461961	0.82[CEU][hapmap]
rs6461964	0.80[CEU][hapmap]
rs6461965	0.83[CEU][hapmap]
rs6461971	0.83[CEU][hapmap]
rs687254	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6970591	0.81[CEU][hapmap]
rs6973237	0.83[CEU][hapmap]
rs757129	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7784257	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7788165	0.80[EUR][1000 genomes]
rs7795313	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7802771	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7802852	0.81[EUR][1000 genomes]
rs7807640	0.85[CEU][hapmap]
rs7810179	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7811764	0.82[EUR][1000 genomes]
rs891876	0.85[CEU][hapmap]
rs989250	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025538	chr7:26482342-27376045	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
2	nsv538805	chr7:26482342-27376045	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
3	nsv5672	chr7:26711462-26757891	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1018125	chr7:26745074-26789814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12700754	SKAP2	cis	Whole Blood	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26705000-26759600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr7:26729000-26756400	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr7:26731800-26779200	Weak transcription	Spleen	Spleen
4	chr7:26732200-26765000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr7:26740400-26782400	Weak transcription	Fetal Intestine Small	intestine
6	chr7:26745000-26780800	Weak transcription	Aorta	Aorta
7	chr7:26745400-26764600	Weak transcription	Adipose Nuclei	Adipose
8	chr7:26745600-26754400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr7:26745800-26759600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr7:26745800-26764600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr7:26746200-26780600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr7:26746600-26777400	Weak transcription	Lung	lung
13	chr7:26747800-26762800	Weak transcription	Primary B cells from peripheral blood	blood
14	chr7:26748000-26764800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr7:26749000-26762600	Weak transcription	GM12878-XiMat	blood
16	chr7:26749200-26779600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr7:26749400-26759800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr7:26749400-26760200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr7:26749600-26781000	Weak transcription	NHEK	skin
20	chr7:26749800-26762600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr7:26750400-26762400	Weak transcription	Fetal Lung	lung
22	chr7:26750400-26812000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr7:26750800-26757000	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr7:26751000-26758000	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr7:26751400-26759600	Weak transcription	Primary B cells from cord blood	blood
26	chr7:26753600-26754400	Enhancers	Fetal Stomach	stomach
27	chr7:26753600-26782200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr7:26754000-26754600	Enhancers	NHLF	lung
29	chr7:26754200-26754600	Enhancers	Osteobl	bone
30	chr7:26754200-26754800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr7:26754200-26780600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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