Variant report

Variant	rs2299104
Chromosome Location	chr7:26749826-26749827
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1023711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11536406	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12055950	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12538196	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12538337	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12672000	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2299100	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3735549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3801817	1.00[CEU][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3801863	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56746976	1.00[EUR][1000 genomes]
rs58941309	1.00[EUR][1000 genomes]
rs62447704	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62447731	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62447733	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62448176	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62448179	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62448195	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62448201	0.91[EUR][1000 genomes]
rs62448202	0.91[EUR][1000 genomes]
rs62448203	0.91[EUR][1000 genomes]
rs6461968	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7782107	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[EUR][1000 genomes]
rs9638840	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]

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

No data

Chromatin state (count:27 , 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	chr7:26729600-26750000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr7:26731800-26779200	Weak transcription	Spleen	Spleen
5	chr7:26732200-26765000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr7:26740400-26782400	Weak transcription	Fetal Intestine Small	intestine
7	chr7:26742800-26750800	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr7:26745000-26780800	Weak transcription	Aorta	Aorta
9	chr7:26745200-26750200	Weak transcription	Fetal Lung	lung
10	chr7:26745400-26764600	Weak transcription	Adipose Nuclei	Adipose
11	chr7:26745600-26754400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr7:26745800-26759600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr7:26745800-26764600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr7:26746200-26780600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr7:26746600-26777400	Weak transcription	Lung	lung
16	chr7:26747800-26752600	Weak transcription	Psoas Muscle	Psoas
17	chr7:26747800-26762800	Weak transcription	Primary B cells from peripheral blood	blood
18	chr7:26748000-26764800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr7:26749000-26762600	Weak transcription	GM12878-XiMat	blood
20	chr7:26749200-26753600	Weak transcription	Fetal Intestine Large	intestine
21	chr7:26749200-26779600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr7:26749400-26751000	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr7:26749400-26759800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr7:26749400-26760200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr7:26749600-26781000	Weak transcription	NHEK	skin
26	chr7:26749800-26751400	Strong transcription	Primary B cells from cord blood	blood
27	chr7:26749800-26762600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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