Variant report

Variant	rs523975
Chromosome Location	chr3:138314463-138314464
allele	C/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:138309173..138314814-chr3:138323140..138328328,8	K562	blood:
2	chr3:138313052..138315422-chr3:138326245..138328582,4	MCF-7	breast:
3	chr3:138313714..138315292-chr3:138315408..138318314,2	K562	blood:
4	chr3:138311550..138315468-chr3:138324471..138329332,12	MCF-7	breast:
5	chr3:138308891..138310571-chr3:138313902..138316460,2	K562	blood:
6	chr3:138312690..138314858-chr3:138552284..138553853,2	K562	blood:
7	chr3:137892183..137893942-chr3:138313140..138314743,2	K562	blood:
8	chr3:138312928..138314956-chr3:138381208..138383898,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000138231	Chromatin interaction
ENSG00000158234	Chromatin interaction
ENSG00000051382	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1068685	1.00[CHB][hapmap]
rs10804658	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1091528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1663554	1.00[CHB][hapmap]
rs1673597	1.00[CHB][hapmap]
rs1679168	0.82[CEU][hapmap]
rs1679174	0.90[AMR][1000 genomes]
rs1679178	1.00[ASW][hapmap]
rs17282752	1.00[JPT][hapmap]
rs191714	1.00[CHB][hapmap]
rs191775	1.00[CHB][hapmap]
rs2347469	0.81[CEU][hapmap]
rs2607796	1.00[CHB][hapmap]
rs361057	1.00[CHB][hapmap]
rs361059	1.00[CHB][hapmap]
rs361060	1.00[CHB][hapmap]
rs361061	1.00[CHB][hapmap]
rs361062	1.00[CHB][hapmap]
rs361063	1.00[CHB][hapmap]
rs361066	1.00[CHB][hapmap]
rs361067	1.00[CHB][hapmap]
rs361071	1.00[CHB][hapmap]
rs361072	1.00[CHB][hapmap]
rs361073	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs361074	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs361075	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs361076	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs361077	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs361080	1.00[CHB][hapmap]
rs361082	1.00[CHB][hapmap]
rs361087	1.00[CHB][hapmap]
rs361088	1.00[CHB][hapmap]
rs361096	1.00[CHB][hapmap]
rs385254	1.00[CHB][hapmap]
rs413147	1.00[CHB][hapmap]
rs4305444	1.00[CHB][hapmap]
rs484698	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs493152	1.00[CHB][hapmap]
rs497900	1.00[CHB][hapmap]
rs500687	1.00[CHB][hapmap]
rs520904	1.00[CHB][hapmap]
rs524164	1.00[CHB][hapmap]
rs531577	1.00[CHB][hapmap]
rs537894	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs558905	1.00[CHB][hapmap]
rs559160	1.00[CHB][hapmap]
rs564455	1.00[CHB][hapmap]
rs600590	1.00[CHB][hapmap]
rs601032	1.00[CHB][hapmap]
rs603723	1.00[CHB][hapmap]
rs624099	1.00[CHB][hapmap]
rs635592	1.00[CHB][hapmap]
rs642258	1.00[ASN][1000 genomes]
rs643620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7643722	1.00[CHB][hapmap]
rs773045	1.00[CHB][hapmap]
rs773456	1.00[ASN][1000 genomes]
rs774015	1.00[CHB][hapmap]
rs811322	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9822714	1.00[CHB][hapmap]
rs9848938	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv999041	chr3:138148812-138347988	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	esv3429877	chr3:138272946-138325019	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs523975	FAIM	cis	parietal	SCAN
rs523975	CEP70	cis	cerebellum	SCAN
rs523975	A4GNT	cis	parietal	SCAN
rs523975	ARMC8	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138311600-138315000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr3:138313600-138327200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:138313800-138314600	Enhancers	Fetal Thymus	thymus
4	chr3:138313800-138314800	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr3:138313800-138316000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:138313800-138316200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr3:138313800-138319000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:138313800-138327200	Weak transcription	Psoas Muscle	Psoas
9	chr3:138314000-138315200	Enhancers	Primary hematopoietic stem cells	blood
10	chr3:138314000-138315800	Weak transcription	Gastric	stomach
11	chr3:138314000-138315800	Weak transcription	Pancreas	Pancrea
12	chr3:138314000-138316000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr3:138314000-138316000	Weak transcription	Liver	Liver
14	chr3:138314000-138319000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:138314000-138319000	Weak transcription	Osteobl	bone
16	chr3:138314000-138319200	Weak transcription	Adipose Nuclei	Adipose
17	chr3:138314000-138321400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:138314000-138327000	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr3:138314000-138327200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr3:138314200-138314600	Enhancers	Dnd41	blood
21	chr3:138314200-138315000	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr3:138314200-138315400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:138314200-138315800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:138314200-138316000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr3:138314200-138316000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr3:138314200-138316000	Weak transcription	HepG2	liver
27	chr3:138314200-138319200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:138314200-138319400	Weak transcription	Stomach Mucosa	stomach
29	chr3:138314200-138327000	Weak transcription	Brain Hippocampus Middle	brain
30	chr3:138314400-138315800	Weak transcription	GM12878-XiMat	blood

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