Variant report

Variant	rs6889684
Chromosome Location	chr5:1601786-1601787
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:1554098..1555865-chr5:1599469..1601874,2	MCF-7	breast:
2	chr5:1594293..1596360-chr5:1601095..1603378,2	MCF-7	breast:
3	chr5:1480807..1481384-chr5:1601774..1602288,2	MCF-7	breast:
4	chr5:1521482..1523114-chr5:1599909..1603157,3	MCF-7	breast:
5	chr5:1601386..1602232-chr5:1644668..1645654,3	MCF-7	breast:
6	chr5:1601351..1602385-chr5:1641606..1642321,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271119	Chromatin interaction
ENSG00000185986	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10512659	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11133831	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11948870	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11951409	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11951807	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11951980	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11952238	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11953233	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11954077	1.00[ASN][1000 genomes]
rs11955967	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11957991	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11958097	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2883372	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4415117	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55864560	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55867519	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55957581	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56185279	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58452381	1.00[ASN][1000 genomes]
rs58687576	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59610035	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59656356	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59806631	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61340395	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6867199	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6869310	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6870117	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6871261	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6872202	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6884318	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6888170	1.00[ASN][1000 genomes]
rs6888910	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6889629	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6891099	1.00[ASN][1000 genomes]
rs6898538	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72717589	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72717593	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72717595	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72717596	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72717598	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72717600	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73732121	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73732122	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73732123	0.81[AMR][1000 genomes]
rs73732124	1.00[ASN][1000 genomes]
rs73732134	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7708447	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7716004	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7725592	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7728463	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7728632	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7729323	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7732756	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7736524	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7736669	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7737033	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7737331	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6889684	SDHAP3	cis	Whole Blood	GTEx
rs6889684	SDHAP3	cis	Esophagus Muscularis	GTEx
rs6889684	SDHAP3	cis	Esophagus Mucosa	GTEx
rs6889684	LOC728613///PDCD6	Cis_1M	lymphoblastoid	RTeQTL
rs6889684	CTD-2012J19.3	cis	Esophagus Mucosa	GTEx
rs6889684	SDHAP3	cis	Artery Tibial	GTEx
rs6889684	RP11-43F13.1	cis	Whole Blood	GTEx
rs6889684	SDHAP3	cis	Thyroid	GTEx
rs6889684	SDHAP3	cis	Nerve Tibial	GTEx

Chromatin state (count:56 , 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	chr5:1595200-1608200	Weak transcription	Primary T cells from cord blood	blood
4	chr5:1595200-1610600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr5:1595200-1610600	Weak transcription	Aorta	Aorta
6	chr5:1595200-1610800	Weak transcription	Fetal Intestine Small	intestine
7	chr5:1595200-1610800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr5:1595200-1618400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr5:1595200-1618400	Weak transcription	Liver	Liver
10	chr5:1595200-1618400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr5:1595200-1618600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:1595200-1632800	Weak transcription	Brain Angular Gyrus	brain
13	chr5:1595200-1632800	Weak transcription	Right Ventricle	heart
14	chr5:1595400-1607400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr5:1595400-1607400	Weak transcription	Fetal Muscle Leg	muscle
16	chr5:1595400-1607800	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr5:1595400-1608200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr5:1595400-1619200	Weak transcription	GM12878-XiMat	blood
19	chr5:1595400-1619400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr5:1595400-1633200	Weak transcription	Primary B cells from cord blood	blood
21	chr5:1595400-1633200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr5:1595400-1633200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr5:1595400-1633200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr5:1595600-1607400	Weak transcription	Fetal Lung	lung
25	chr5:1595800-1617200	Weak transcription	Thymus	Thymus
26	chr5:1597600-1602800	Weak transcription	Fetal Stomach	stomach
27	chr5:1597600-1607400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr5:1597600-1610600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr5:1597600-1612000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr5:1597600-1618800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr5:1597600-1619200	Weak transcription	Fetal Brain Female	brain
32	chr5:1597600-1621400	Weak transcription	Brain Substantia Nigra	brain
33	chr5:1597600-1621800	Weak transcription	Ovary	ovary
34	chr5:1597600-1626400	Weak transcription	Adipose Nuclei	Adipose
35	chr5:1597600-1632600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr5:1597600-1632800	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr5:1597600-1632800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr5:1597600-1633000	Weak transcription	Brain Hippocampus Middle	brain
39	chr5:1597800-1602000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr5:1599200-1602000	Strong transcription	Dnd41	blood
41	chr5:1600000-1607600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr5:1600800-1601800	Strong transcription	Primary B cells from peripheral blood	blood
43	chr5:1600800-1603800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr5:1601000-1601800	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr5:1601000-1602000	Enhancers	H1 Cell Line	embryonic stem cell
46	chr5:1601200-1601800	Enhancers	H9 Cell Line	embryonic stem cell
47	chr5:1601200-1601800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr5:1601200-1601800	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr5:1601200-1601800	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr5:1601200-1601800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell

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