Variant report

Variant	rs12634716
Chromosome Location	chr3:138582751-138582752
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 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	chr3:137891312..137893819-chr3:138582385..138585243,2	K562	blood:
14	chr3:138552566..138554608-chr3:138580222..138582858,2	MCF-7	breast:
15	chr3:138550984..138557271-chr3:138577921..138584342,10	K562	blood:

No data

Variant related genes	Relation type
ENSG00000138231	Chromatin interaction
ENSG00000051382	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11721001	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12495319	0.87[EUR][1000 genomes]
rs35392301	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs68094276	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9809657	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9820131	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9879628	0.88[AMR][1000 genomes];0.90[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12634716	CEP70	Cis_1M	lymphoblastoid	RTeQTL
rs12634716	PIK3CB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 50 per page) page: 1

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	chr3:138579800-138582800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr3:138579800-138583000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:138580000-138582800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:138580000-138583600	Enhancers	Pancreas	Pancrea
9	chr3:138580400-138582800	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr3:138580400-138582800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:138580400-138583000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:138580400-138585000	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr3:138581200-138582800	Enhancers	Placenta Amnion	Placenta Amnion
14	chr3:138581200-138582800	Flanking Active TSS	A549	lung
15	chr3:138581400-138582800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
16	chr3:138581400-138582800	Flanking Active TSS	K562	blood
17	chr3:138582000-138582800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr3:138582000-138583000	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr3:138582200-138582800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:138582200-138582800	Enhancers	HUVEC	blood vessel
21	chr3:138582200-138583000	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr3:138582200-138583000	Flanking Active TSS	HepG2	liver
23	chr3:138582400-138582800	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr3:138582400-138582800	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr3:138582400-138582800	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr3:138582400-138582800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:138582400-138583000	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr3:138582400-138583000	Enhancers	HMEC	breast
29	chr3:138582400-138583600	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr3:138582400-138584800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:138582600-138582800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:138582600-138582800	Enhancers	Hela-S3	cervix
33	chr3:138582600-138583000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:138582600-138583000	Enhancers	Duodenum Mucosa	Duodenum
35	chr3:138582600-138583000	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr3:138582600-138583000	Weak transcription	Right Atrium	heart
37	chr3:138582600-138583000	Enhancers	Stomach Mucosa	stomach
38	chr3:138582600-138583000	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr3:138582600-138583000	Enhancers	NHEK	skin
40	chr3:138582600-138583200	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr3:138582600-138584600	Weak transcription	Left Ventricle	heart
42	chr3:138582600-138585200	Weak transcription	Brain Angular Gyrus	brain
43	chr3:138582600-138586200	Weak transcription	Adipose Nuclei	Adipose
44	chr3:138582600-138586200	Weak transcription	Fetal Muscle Leg	muscle
45	chr3:138582600-138592400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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