Variant report

Variant	rs6771889
Chromosome Location	chr3:48194326-48194327
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47886059..47888600-chr3:48194034..48195551,2	K562	blood:
2	chr3:47873536..47875559-chr3:48191736..48194650,2	MCF-7	breast:
3	chr3:47865781..47868282-chr3:48191820..48194730,2	K562	blood:

Variant related genes	Relation type
ENSG00000132153	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 35 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11130157	0.88[EUR][1000 genomes]
rs11711766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720151	0.82[MEX][hapmap];0.81[TSI][hapmap]
rs12493256	0.96[EUR][1000 genomes]
rs12494304	0.96[EUR][1000 genomes]
rs12494396	0.91[EUR][1000 genomes]
rs12495221	0.97[EUR][1000 genomes]
rs12496784	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12633518	0.82[YRI][hapmap]
rs13099560	0.80[EUR][1000 genomes]
rs1380053	0.82[YRI][hapmap]
rs34422222	0.87[EUR][1000 genomes]
rs34513961	0.81[EUR][1000 genomes]
rs34648110	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35142214	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4858892	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62262998	0.88[EUR][1000 genomes]
rs62263001	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6442105	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6442106	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6442107	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6442108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6442109	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6766754	1.00[CEU][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6771787	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6775114	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6796490	0.80[EUR][1000 genomes]
rs6797587	0.92[CEU][hapmap];0.80[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6800730	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7374376	1.00[CEU][hapmap];0.88[JPT][hapmap];0.95[EUR][1000 genomes]
rs7429594	0.85[EUR][1000 genomes]
rs7431293	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7617773	0.80[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7642590	0.88[ASW][hapmap]
rs9822496	0.97[EUR][1000 genomes]
rs9825114	0.88[ASW][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs9832957	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529989	chr3:47909480-48301481	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats 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 miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1001056	chr3:47912342-48223849	Genic enhancers Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	esv1827272	chr3:47912703-48260968	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1009243	chr3:47935331-48340448	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv536562	chr3:47935331-48340448	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv1002067	chr3:47996472-48326518	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS 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 miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv876760	chr3:48019258-48197614	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv1004557	chr3:48056534-48256694	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv1012024	chr3:48119229-48242670	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv834682	chr3:48138137-48311122	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:35)

SNP	Gene	Cis/trans	Tissue	Source
rs6771889	ZNF589	cis	Adipose Subcutaneous	GTEx
rs6771889	MRPS18AP1	cis	Stomach	GTEx
rs6771889	ZNF589	cis	Esophagus Mucosa	GTEx
rs6771889	MRPS18AP1	cis	lung	GTEx
rs6771889	ZNF589	cis	lung	GTEx
rs6771889	CDC25A	cis	Artery Tibial	GTEx
rs6771889	MRPS18AP1	cis	Skin Sun Exposed Lower leg	GTEx
rs6771889	ZNF589	cis	cerebellum	SCAN
rs6771889	ZNF589	cis	Whole Blood	GTEx
rs6771889	CDC25A	cis	cerebellum	SCAN
rs6771889	GNAI2	cis	parietal	SCAN
rs6771889	CDC25A	cis	Muscle Skeletal	GTEx
rs6771889	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs6771889	NME6	Cis_1M	lymphoblastoid	RTeQTL
rs6771889	ALS2CL	cis	parietal	SCAN
rs6771889	RBM5	cis	cerebellum	SCAN
rs6771889	MRPS18AP1	cis	Thyroid	GTEx
rs6771889	ZNF589	cis	Artery Tibial	GTEx
rs6771889	CDC25A	cis	Adipose Subcutaneous	GTEx
rs6771889	MRPS18AP1	cis	Nerve Tibial	GTEx
rs6771889	ZNF589	cis	Thyroid	GTEx
rs6771889	UQCRC1	cis	parietal	SCAN
rs6771889	ARIH2	cis	parietal	SCAN
rs6771889	MRPS18AP1	cis	Artery Tibial	GTEx
rs6771889	ZNF589	cis	parietal	SCAN
rs6771889	ZNF589	cis	Skin Sun Exposed Lower leg	GTEx
rs6771889	MRPS18AP1	cis	Adipose Subcutaneous	GTEx
rs6771889	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs6771889	MRPS18AP1	cis	Esophagus Mucosa	GTEx
rs6771889	NME6	cis	Esophagus Muscularis	GTEx
rs6771889	MRPS18AP1	cis	Heart Left Ventricle	GTEx
rs6771889	ZNF589	cis	Nerve Tibial	GTEx
rs6771889	CDC25A	cis	Thyroid	GTEx
rs6771889	NME6	cis	cerebellum	SCAN
rs6771889	MRPS18AP1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48182200-48198400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:48182200-48199400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:48184200-48196400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:48186000-48200200	Weak transcription	Spleen	Spleen
5	chr3:48191600-48194800	Enhancers	Fetal Muscle Trunk	muscle
6	chr3:48192400-48194400	Enhancers	Fetal Muscle Leg	muscle
7	chr3:48192600-48194400	Enhancers	Fetal Heart	heart
8	chr3:48192600-48195000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:48192600-48200200	Weak transcription	Brain Germinal Matrix	brain
10	chr3:48193000-48196200	Weak transcription	NH-A	brain
11	chr3:48193000-48198400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:48193000-48198400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:48193000-48198400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:48193000-48198400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr3:48193000-48198800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr3:48193000-48198800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr3:48193000-48198800	Weak transcription	Fetal Lung	lung
18	chr3:48193000-48199200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:48193000-48199800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:48193000-48205200	Weak transcription	Brain Anterior Caudate	brain
21	chr3:48193000-48205400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr3:48193000-48228400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:48193200-48197600	Weak transcription	Fetal Thymus	thymus
24	chr3:48193200-48197800	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr3:48193200-48200200	Weak transcription	Ovary	ovary
26	chr3:48193200-48205200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr3:48193200-48206800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr3:48193400-48196000	Weak transcription	NHEK	skin
29	chr3:48193400-48199200	Weak transcription	Fetal Stomach	stomach
30	chr3:48193400-48206800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr3:48193400-48210400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr3:48193600-48195600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr3:48193600-48195800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:48193600-48195800	Weak transcription	HMEC	breast
35	chr3:48193600-48196000	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr3:48193600-48196000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:48193600-48196000	Weak transcription	HUVEC	blood vessel
38	chr3:48193600-48197600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:48193600-48199000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr3:48193600-48199000	Weak transcription	GM12878-XiMat	blood
41	chr3:48193600-48200000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr3:48193600-48202800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr3:48193600-48205200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr3:48193600-48228200	Weak transcription	Pancreas	Pancrea
45	chr3:48193800-48195400	Weak transcription	Stomach Mucosa	stomach
46	chr3:48193800-48196000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:48193800-48198400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr3:48193800-48199600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:48193800-48200000	Weak transcription	Fetal Intestine Large	intestine
50	chr3:48193800-48200000	Weak transcription	HSMM	muscle

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