Variant report

Variant	rs13072891
Chromosome Location	chr3:20028570-20028571
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:20027209..20028836-chr3:20081202..20083011,2	K562	blood:
2	chr3:20027598..20030041-chr3:20034679..20036338,2	K562	blood:
3	chr3:20027470..20029591-chr3:20033923..20036338,3	K562	blood:
4	chr3:20022682..20025378-chr3:20026127..20028940,2	MCF-7	breast:
5	chr3:20026329..20028709-chr3:20079789..20082702,2	K562	blood:

Variant related genes	Relation type
ENSG00000114166	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 12 )

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

rs_ID	r²[population]
rs11128927	0.81[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs11128928	0.90[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs11128929	0.90[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs11128930	0.90[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs11128931	0.90[CHB][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs1143451	0.91[ASN][1000 genomes]
rs12629485	0.90[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs13065319	0.90[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs13076973	0.86[ASN][1000 genomes]
rs13077307	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13078505	0.89[ASN][1000 genomes]
rs13082980	0.88[ASN][1000 genomes]
rs13086159	0.90[ASN][1000 genomes]
rs13089853	0.86[ASN][1000 genomes]
rs13098388	0.86[ASN][1000 genomes]
rs17181400	0.81[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs17181862	0.91[ASN][1000 genomes]
rs17796115	0.86[ASN][1000 genomes]
rs34305656	0.86[ASN][1000 genomes]
rs34343204	0.91[ASN][1000 genomes]
rs34417128	0.91[ASN][1000 genomes]
rs35175665	0.91[ASN][1000 genomes]
rs35482904	0.96[ASN][1000 genomes]
rs35713165	0.86[ASN][1000 genomes]
rs4858121	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs58859849	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59086970	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59608170	0.86[ASN][1000 genomes]
rs60255931	0.88[ASN][1000 genomes]
rs62241278	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6796425	0.90[ASN][1000 genomes]
rs7614695	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615145	0.86[ASN][1000 genomes]
rs7618928	0.86[ASN][1000 genomes]
rs7633940	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7634934	0.90[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs7646128	0.86[ASN][1000 genomes]
rs9877801	0.88[ASN][1000 genomes]
rs9878879	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1828161	chr3:19547184-20062060	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription 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	17 gene(s)	inside rSNPs	diseases
2	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv1826570	chr3:19579860-20077414	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats 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	17 gene(s)	inside rSNPs	diseases
6	esv1826254	chr3:19592688-20042834	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers 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 target site	15 gene(s)	inside rSNPs	diseases
9	esv1825988	chr3:19976375-20102773	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
11	nsv997486	chr3:20006702-20113989	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
12	esv1829542	chr3:20009231-20384627	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs13072891	EFHB	cis	Thyroid	GTEx
rs13072891	RAB5A	cis	cerebellum	SCAN
rs13072891	EFHB	cis	Nerve Tibial	GTEx
rs13072891	EFHB	cis	Whole Blood	GTEx
rs13072891	EFHB	cis	Adipose Subcutaneous	GTEx
rs13072891	RFTN1	cis	cerebellum	SCAN
rs13072891	EFHB	cis	parietal	SCAN
rs13072891	EFHB	cis	Skin Sun Exposed Lower leg	GTEx
rs13072891	EFHB	cis	Artery Tibial	GTEx
rs13072891	EFHB	cis	Esophagus Mucosa	GTEx
rs13072891	EFHB	cis	cerebellum	SCAN
rs13072891	EFHB	cis	Esophagus Muscularis	GTEx

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20008800-20035600	Weak transcription	Psoas Muscle	Psoas
2	chr3:20012400-20033600	Weak transcription	Fetal Brain Male	brain
3	chr3:20015200-20030000	Strong transcription	Fetal Thymus	thymus
4	chr3:20021800-20029400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:20023000-20045800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:20023400-20029000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:20024000-20031200	Weak transcription	HSMM	muscle
8	chr3:20024000-20041400	Weak transcription	Ovary	ovary
9	chr3:20024200-20028600	Weak transcription	Colonic Mucosa	Colon
10	chr3:20024200-20030600	Weak transcription	Hela-S3	cervix
11	chr3:20024200-20031000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr3:20024200-20031200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:20024200-20031800	Weak transcription	Left Ventricle	heart
14	chr3:20024200-20033200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr3:20024200-20033400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:20024200-20036800	Weak transcription	Aorta	Aorta
17	chr3:20024200-20051400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:20024400-20028600	Weak transcription	Brain Substantia Nigra	brain
19	chr3:20024400-20029000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr3:20024400-20029200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr3:20024400-20029800	Weak transcription	Spleen	Spleen
22	chr3:20024400-20030600	Weak transcription	Thymus	Thymus
23	chr3:20024400-20034000	Weak transcription	Brain Germinal Matrix	brain
24	chr3:20024600-20029000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:20024800-20029000	Weak transcription	Fetal Intestine Small	intestine
26	chr3:20024800-20030800	Weak transcription	Fetal Stomach	stomach
27	chr3:20024800-20031600	Weak transcription	Lung	lung
28	chr3:20024800-20031800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:20025400-20028600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr3:20025400-20028600	Weak transcription	GM12878-XiMat	blood
31	chr3:20025400-20029000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr3:20025400-20029000	Weak transcription	NHDF-Ad	bronchial
33	chr3:20025400-20029600	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr3:20025400-20030600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr3:20025400-20031800	Weak transcription	Fetal Brain Female	brain
36	chr3:20025400-20033200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:20025600-20028600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr3:20025600-20028600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr3:20025600-20029000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr3:20025600-20029000	Weak transcription	K562	blood
41	chr3:20025600-20033400	Weak transcription	Brain Angular Gyrus	brain
42	chr3:20025800-20029000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:20025800-20029200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr3:20025800-20029200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:20025800-20029800	Weak transcription	Brain Anterior Caudate	brain
46	chr3:20025800-20030400	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr3:20025800-20030600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr3:20026000-20028800	Weak transcription	Stomach Smooth Muscle	stomach
49	chr3:20026200-20029000	Weak transcription	Fetal Muscle Leg	muscle
50	chr3:20026200-20031000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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