Variant report

Variant	rs2937009
Chromosome Location	chr5:1610773-1610774
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:1610767-1611149	GM12878	blood:	n/a	n/a
2	POLR2A	chr5:1610555-1610951	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000232615	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12055347	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12651871	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12658142	0.83[ASN][1000 genomes]
rs1827192	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1827193	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2937005	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2937006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2937012	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2937014	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2937016	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2937019	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2962034	0.81[ASN][1000 genomes]
rs2962047	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35549554	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4246747	0.81[ASN][1000 genomes]
rs4415118	0.81[ASN][1000 genomes]
rs56775155	0.86[ASN][1000 genomes]
rs59875755	0.87[ASN][1000 genomes]
rs6554903	0.82[ASN][1000 genomes]
rs6891307	0.90[ASN][1000 genomes]
rs6892057	0.81[AFR][1000 genomes]
rs6898387	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933805	chr5:1450724-1941619	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv880740	chr5:1468287-1671200	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
3	nsv881554	chr5:1468287-1696932	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
4	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
5	nsv881096	chr5:1503610-1671200	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
6	nsv596879	chr5:1519079-1624351	Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers 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	29 gene(s)	inside rSNPs	diseases
7	nsv10657	chr5:1544428-1633373	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv596885	chr5:1552255-1624351	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv964815	chr5:1608931-1639317	Strong transcription Active TSS Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1595000-1626600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:1595000-1634000	Weak transcription	Stomach Mucosa	stomach
3	chr5:1595200-1610800	Weak transcription	Fetal Intestine Small	intestine
4	chr5:1595200-1610800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr5:1595200-1618400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr5:1595200-1618400	Weak transcription	Liver	Liver
7	chr5:1595200-1618400	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr5:1595200-1618600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr5:1595200-1632800	Weak transcription	Brain Angular Gyrus	brain
10	chr5:1595200-1632800	Weak transcription	Right Ventricle	heart
11	chr5:1595400-1619200	Weak transcription	GM12878-XiMat	blood
12	chr5:1595400-1619400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr5:1595400-1633200	Weak transcription	Primary B cells from cord blood	blood
14	chr5:1595400-1633200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr5:1595400-1633200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr5:1595400-1633200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr5:1595800-1617200	Weak transcription	Thymus	Thymus
18	chr5:1597600-1612000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr5:1597600-1618800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr5:1597600-1619200	Weak transcription	Fetal Brain Female	brain
21	chr5:1597600-1621400	Weak transcription	Brain Substantia Nigra	brain
22	chr5:1597600-1621800	Weak transcription	Ovary	ovary
23	chr5:1597600-1626400	Weak transcription	Adipose Nuclei	Adipose
24	chr5:1597600-1632600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr5:1597600-1632800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr5:1597600-1632800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr5:1597600-1633000	Weak transcription	Brain Hippocampus Middle	brain
28	chr5:1601400-1632800	Weak transcription	Hela-S3	cervix
29	chr5:1601600-1617200	Weak transcription	Fetal Intestine Large	intestine
30	chr5:1601600-1618000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr5:1601800-1616600	Weak transcription	Primary B cells from peripheral blood	blood
32	chr5:1601800-1616800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr5:1601800-1620600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr5:1602000-1612000	Weak transcription	Dnd41	blood
35	chr5:1604600-1617000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr5:1606200-1633200	Weak transcription	Brain Anterior Caudate	brain
37	chr5:1607200-1618400	Weak transcription	Lung	lung
38	chr5:1607600-1611800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr5:1607600-1621000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr5:1607600-1626600	Weak transcription	Fetal Muscle Trunk	muscle
41	chr5:1607800-1617200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr5:1607800-1623800	Weak transcription	Fetal Muscle Leg	muscle
43	chr5:1608000-1620600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr5:1608000-1624200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr5:1608200-1613600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr5:1608200-1619000	Weak transcription	Right Atrium	heart
47	chr5:1608400-1626400	Weak transcription	Pancreas	Pancrea
48	chr5:1608600-1612000	Weak transcription	Primary T cells from cord blood	blood
49	chr5:1608600-1620800	Weak transcription	Brain Germinal Matrix	brain
50	chr5:1608800-1611800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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