Variant report

Variant	rs13061496
Chromosome Location	chr3:138582432-138582433
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:138581629..138583620-chr3:138597045..138599792,2	K562	blood:
2	chr3:138552300..138556689-chr3:138579169..138582994,10	MCF-7	breast:
3	chr3:138579482..138585214-chr3:138633331..138636801,5	K562	blood:
4	chr3:138573362..138576869-chr3:138581284..138584283,3	MCF-7	breast:
5	chr3:138580973..138583451-chr3:138633177..138634854,2	MCF-7	breast:
6	chr3:138581227..138583620-chr3:138597045..138599792,3	K562	blood:
7	chr3:138581454..138585634-chr3:138592021..138596158,7	K562	blood:
8	chr3:138580257..138585634-chr3:138593415..138596528,8	K562	blood:
9	chr3:138552063..138557271-chr3:138580166..138583961,9	K562	blood:
10	chr3:138582033..138584014-chr3:138634089..138636895,3	K562	blood:
11	chr3:138572750..138576892-chr3:138578967..138583647,7	K562	blood:
12	chr3:138443736..138445384-chr3:138580808..138583344,2	K562	blood:
13	chr3:138572929..138574739-chr3:138578967..138582635,3	K562	blood:
14	chr3:137891312..137893819-chr3:138582385..138585243,2	K562	blood:
15	chr3:138552566..138554608-chr3:138580222..138582858,2	MCF-7	breast:
16	chr3:138550984..138557271-chr3:138577921..138584342,10	K562	blood:
17	chr3:138580906..138582656-chr3:138587633..138589906,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000051382	Chromatin interaction
ENSG00000138231	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10804659	0.95[EUR][1000 genomes]
rs10935288	0.89[EUR][1000 genomes]
rs11706016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706291	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11708762	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11711360	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11720178	0.92[CEU][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap]
rs11924479	0.85[EUR][1000 genomes]
rs12497815	0.94[EUR][1000 genomes]
rs12631035	0.96[CEU][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12633714	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12635713	0.83[EUR][1000 genomes]
rs13072146	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13077455	0.87[EUR][1000 genomes]
rs13100110	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1663554	0.85[CEU][hapmap]
rs17484361	0.90[EUR][1000 genomes]
rs191714	0.92[CEU][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap]
rs191775	0.92[CEU][hapmap]
rs2881900	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs28826701	0.86[ASN][1000 genomes]
rs35514824	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs361059	0.92[CEU][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs361060	0.92[CEU][hapmap]
rs361061	0.92[CEU][hapmap]
rs361062	0.92[CEU][hapmap]
rs361063	0.92[CEU][hapmap]
rs361066	0.92[CEU][hapmap];0.82[TSI][hapmap]
rs361067	0.92[CEU][hapmap]
rs361071	0.92[CEU][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs361072	0.92[CEU][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs361080	0.92[CEU][hapmap];0.80[MEX][hapmap]
rs361082	0.92[CEU][hapmap]
rs361087	0.85[CEU][hapmap]
rs361088	0.92[CEU][hapmap]
rs361096	0.85[CEU][hapmap]
rs385254	0.92[CEU][hapmap];0.84[TSI][hapmap]
rs413147	0.92[CEU][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap]
rs4305444	0.92[CEU][hapmap]
rs4405948	0.85[EUR][1000 genomes]
rs4894358	0.84[EUR][1000 genomes]
rs4894359	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs493152	0.85[CEU][hapmap]
rs497900	0.92[CEU][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs500687	0.92[CEU][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap]
rs524164	0.92[CEU][hapmap];0.84[TSI][hapmap]
rs531577	0.85[CEU][hapmap]
rs558905	0.92[CEU][hapmap];0.84[TSI][hapmap]
rs564455	0.92[CEU][hapmap];0.84[TSI][hapmap]
rs62282204	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282207	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6439817	0.91[CEU][hapmap]
rs6439828	0.85[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.89[TSI][hapmap]
rs6773514	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs6776833	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6784610	0.92[CEU][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs6791627	0.89[EUR][1000 genomes]
rs6794270	0.81[EUR][1000 genomes]
rs6800801	0.82[EUR][1000 genomes]
rs71312597	0.88[AMR][1000 genomes]
rs7613579	0.96[CEU][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7628172	0.95[EUR][1000 genomes]
rs7634571	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7643722	0.92[CEU][hapmap];0.84[TSI][hapmap]
rs7646689	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7650967	0.96[CEU][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes]
rs9289566	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs9647336	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs9647337	0.92[CEU][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs9812318	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9813576	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9817727	0.95[EUR][1000 genomes]
rs9818354	0.82[EUR][1000 genomes]
rs9821694	0.92[CEU][hapmap]
rs9822500	0.93[EUR][1000 genomes]
rs9822714	0.92[CEU][hapmap]
rs9834963	0.92[CEU][hapmap]
rs9851887	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9855727	0.87[EUR][1000 genomes]
rs9870355	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9871842	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9877108	0.80[EUR][1000 genomes]
rs9879784	0.92[CEU][hapmap]
rs9881861	0.86[ASN][1000 genomes]
rs9882957	0.87[EUR][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	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer 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	38 gene(s)	inside rSNPs	diseases
2	nsv1013074	chr3:138213166-138737688	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1002612	chr3:138213274-138831792	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv536726	chr3:138213274-138831792	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1009726	chr3:138219923-138737688	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv869205	chr3:138248190-138775288	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv868955	chr3:138248190-138848947	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv591854	chr3:138348081-138764229	Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv1010514	chr3:138365640-138737688	Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv1000927	chr3:138423543-138632596	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv917964	chr3:138440701-138699084	Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13061496	CEP70	Cis_1M	lymphoblastoid	RTeQTL
rs13061496	ESYT3	cis	cerebellum	SCAN
rs13061496	FAIM	cis	parietal	SCAN
rs13061496	PIK3CB	Cis_1M	lymphoblastoid	RTeQTL
rs13061496	FAIM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138579400-138583800	Enhancers	Fetal Intestine Large	intestine
2	chr3:138579600-138583000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:138579600-138583600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:138579600-138583800	Enhancers	Fetal Intestine Small	intestine
5	chr3:138579800-138582600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:138579800-138582600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:138579800-138582600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:138579800-138582800	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr3:138579800-138583000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:138580000-138582800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:138580000-138583600	Enhancers	Pancreas	Pancrea
12	chr3:138580400-138582600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:138580400-138582600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:138580400-138582600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr3:138580400-138582600	Enhancers	Fetal Muscle Leg	muscle
16	chr3:138580400-138582600	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr3:138580400-138582800	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr3:138580400-138582800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:138580400-138583000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:138580400-138585000	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr3:138580800-138582600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr3:138580800-138582600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:138580800-138582600	Enhancers	NHDF-Ad	bronchial
24	chr3:138580800-138582600	Enhancers	NHLF	lung
25	chr3:138581000-138582600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:138581000-138582600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:138581000-138582600	Enhancers	Left Ventricle	heart
28	chr3:138581200-138582600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:138581200-138582600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:138581200-138582600	Enhancers	Liver	Liver
31	chr3:138581200-138582600	Enhancers	Brain Angular Gyrus	brain
32	chr3:138581200-138582600	Flanking Active TSS	Duodenum Mucosa	Duodenum
33	chr3:138581200-138582600	Enhancers	Placenta	Placenta
34	chr3:138581200-138582600	Enhancers	HSMM	muscle
35	chr3:138581200-138582600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr3:138581200-138582800	Enhancers	Placenta Amnion	Placenta Amnion
37	chr3:138581200-138582800	Flanking Active TSS	A549	lung
38	chr3:138581400-138582600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:138581400-138582600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:138581400-138582600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:138581400-138582600	Enhancers	Fetal Kidney	kidney
42	chr3:138581400-138582600	Enhancers	Right Atrium	heart
43	chr3:138581400-138582600	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr3:138581400-138582600	Enhancers	GM12878-XiMat	blood
45	chr3:138581400-138582600	Flanking Active TSS	Hela-S3	cervix
46	chr3:138581400-138582800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
47	chr3:138581400-138582800	Flanking Active TSS	K562	blood
48	chr3:138581600-138582600	Enhancers	Fetal Heart	heart
49	chr3:138581600-138582600	Enhancers	Right Ventricle	heart
50	chr3:138581600-138582600	Enhancers	HSMMtube	muscle

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