Variant report

Variant	rs6587917
Chromosome Location	chr1:61825664-61825665
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11207728	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1125778	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12066006	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12134760	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12741051	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12758060	0.93[ASN][1000 genomes]
rs1344420	0.96[ASN][1000 genomes]
rs1344421	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1474873	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2103882	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2180198	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2180199	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2180200	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2207788	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2364467	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2886080	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41423747	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs4406666	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4915735	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4915737	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4915738	0.82[ASN][1000 genomes]
rs6587918	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6587919	1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6587920	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6587921	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6662305	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6673795	0.96[ASN][1000 genomes]
rs6674884	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6697762	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6697777	0.96[ASN][1000 genomes]
rs6697913	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6697955	0.93[ASN][1000 genomes]
rs7512491	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7526670	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7528918	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs7553582	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9436206	0.81[AMR][1000 genomes]
rs9436635	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9436637	0.88[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv994970	chr1:61693951-62199657	Strong transcription Enhancers Weak transcription Active TSS Flanking 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	19 gene(s)	inside rSNPs	diseases
2	nsv1006142	chr1:61696142-62119763	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv534980	chr1:61696142-62119763	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv916868	chr1:61700430-62119762	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1001052	chr1:61702011-62090670	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv817402	chr1:61703965-62119762	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1010797	chr1:61703966-62125970	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv530494	chr1:61723918-62084045	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
9	nsv1000294	chr1:61746280-62350718	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	nsv1014023	chr1:61788310-61859074	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv534981	chr1:61788310-61859074	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:61804400-61851400	Weak transcription	Small Intestine	intestine
2	chr1:61804400-61854600	Weak transcription	Placenta	Placenta
3	chr1:61805800-61848800	Weak transcription	Pancreas	Pancrea
4	chr1:61810200-61827600	Weak transcription	Brain Germinal Matrix	brain
5	chr1:61810400-61828000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:61810600-61828000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:61810600-61831600	Weak transcription	Stomach Mucosa	stomach
8	chr1:61810800-61827800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr1:61813800-61829800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:61814000-61848800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:61814600-61841200	Weak transcription	Psoas Muscle	Psoas
12	chr1:61814600-61848800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:61814800-61827800	Weak transcription	Brain Substantia Nigra	brain
14	chr1:61818400-61827400	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr1:61818600-61837600	Weak transcription	Fetal Brain Male	brain
16	chr1:61818800-61835800	Weak transcription	Esophagus	oesophagus
17	chr1:61819000-61832800	Weak transcription	Brain Angular Gyrus	brain
18	chr1:61819000-61848800	Weak transcription	Lung	lung
19	chr1:61819200-61832800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr1:61820600-61827600	Weak transcription	Brain Hippocampus Middle	brain
21	chr1:61820600-61834600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr1:61820600-61836400	Weak transcription	Duodenum Mucosa	Duodenum
23	chr1:61820600-61840600	Weak transcription	NHEK	skin
24	chr1:61820600-61848800	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr1:61821000-61827600	Strong transcription	Fetal Muscle Leg	muscle
26	chr1:61822200-61827400	Strong transcription	HepG2	liver
27	chr1:61822600-61828200	Strong transcription	Fetal Intestine Large	intestine
28	chr1:61822800-61826200	Strong transcription	Fetal Stomach	stomach
29	chr1:61822800-61831600	Strong transcription	Liver	Liver
30	chr1:61823000-61828200	Strong transcription	Fetal Muscle Trunk	muscle
31	chr1:61823200-61826400	Weak transcription	Colonic Mucosa	Colon
32	chr1:61823200-61828600	Strong transcription	Stomach Smooth Muscle	stomach
33	chr1:61823400-61828000	Weak transcription	Fetal Kidney	kidney
34	chr1:61823400-61854800	Weak transcription	Spleen	Spleen
35	chr1:61823600-61827600	Weak transcription	Fetal Heart	heart
36	chr1:61824200-61826200	Strong transcription	Fetal Intestine Small	intestine
37	chr1:61824200-61827200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:61824400-61827000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr1:61824400-61828200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr1:61824400-61828200	Strong transcription	Fetal Lung	lung
41	chr1:61824600-61826400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:61824600-61826400	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr1:61824600-61827000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr1:61824600-61827400	Strong transcription	Colon Smooth Muscle	Colon
45	chr1:61824800-61826400	Strong transcription	Skeletal Muscle Male	skeletal muscle
46	chr1:61824800-61827000	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr1:61824800-61827000	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr1:61824800-61834000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr1:61825000-61826000	Weak transcription	Left Ventricle	heart
50	chr1:61825000-61827600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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