Variant report

Variant	rs12970514
Chromosome Location	chr18:9585337-9585338
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:9584648..9586476-chr18:9589220..9590730,2	K562	blood:
2	chr18:9577278..9579746-chr18:9582108..9585693,4	K562	blood:
3	chr18:9583998..9586737-chr18:9586977..9590180,4	MCF-7	breast:
4	chr18:9582357..9586836-chr18:9613591..9615895,4	K562	blood:
5	chr18:9584735..9586577-chr18:9599877..9602634,2	K562	blood:
6	chr18:9584254..9588034-chr18:9613364..9615601,3	MCF-7	breast:
7	chr18:9580164..9581759-chr18:9584185..9586548,2	K562	blood:

Variant related genes	Relation type
ENSG00000154845	Chromatin interaction
ENSG00000263627	Chromatin interaction
ENSG00000266541	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1596381	0.85[JPT][hapmap]
rs2867167	0.82[JPT][hapmap]
rs609427	0.82[CEU][hapmap]
rs6506676	1.00[JPT][hapmap]
rs7233980	1.00[JPT][hapmap]
rs8093596	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916373	chr18:9026803-9592201	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv833585	chr18:9401630-9597291	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	esv3693417	chr18:9512985-9693638	Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv458024	chr18:9558240-9828448	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv576448	chr18:9558240-9828448	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	nsv543644	chr18:9576145-9612516	Strong transcription Enhancers Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12970514	AFG3L2	cis	cerebellum	SCAN
rs12970514	SEH1L	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9545800-9595200	Strong transcription	Dnd41	blood
2	chr18:9551000-9612200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr18:9553800-9613600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr18:9559000-9586800	Weak transcription	Small Intestine	intestine
5	chr18:9559600-9587000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr18:9563600-9591600	Weak transcription	Colonic Mucosa	Colon
7	chr18:9563600-9594800	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr18:9565200-9594200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr18:9566800-9592600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr18:9566800-9594600	Strong transcription	HSMM	muscle
11	chr18:9568600-9587600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr18:9570400-9594400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr18:9572200-9587400	Weak transcription	Ovary	ovary
14	chr18:9575800-9592800	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr18:9576000-9594400	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr18:9576200-9586800	Weak transcription	Brain Hippocampus Middle	brain
17	chr18:9576200-9587600	Weak transcription	Brain Substantia Nigra	brain
18	chr18:9576200-9589000	Strong transcription	NHDF-Ad	bronchial
19	chr18:9576200-9594000	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr18:9576200-9597800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr18:9577200-9585400	Strong transcription	Fetal Muscle Trunk	muscle
22	chr18:9577600-9594400	Weak transcription	Stomach Mucosa	stomach
23	chr18:9578200-9589200	Strong transcription	Primary B cells from cord blood	blood
24	chr18:9578400-9587800	Weak transcription	Gastric	stomach
25	chr18:9578400-9595200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr18:9578600-9590800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr18:9578800-9594800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr18:9579000-9585800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr18:9579000-9592600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr18:9579000-9593800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr18:9579600-9585600	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr18:9579600-9591400	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr18:9579600-9594000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr18:9579800-9589000	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr18:9579800-9593800	Strong transcription	HUVEC	blood vessel
36	chr18:9580000-9586400	Weak transcription	NHLF	lung
37	chr18:9580000-9586800	Weak transcription	A549	lung
38	chr18:9580400-9586800	Weak transcription	Stomach Smooth Muscle	stomach
39	chr18:9580600-9585600	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr18:9580800-9587800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr18:9581000-9587000	Weak transcription	Spleen	Spleen
42	chr18:9581000-9594000	Weak transcription	Esophagus	oesophagus
43	chr18:9581000-9595400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr18:9581200-9586800	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr18:9581200-9587400	Weak transcription	Lung	lung
46	chr18:9581200-9587600	Weak transcription	Right Ventricle	heart
47	chr18:9581200-9587600	Weak transcription	Thymus	Thymus
48	chr18:9581200-9592800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr18:9581200-9593800	Weak transcription	Aorta	Aorta
50	chr18:9581400-9585600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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