Variant report

Variant	rs34569561
Chromosome Location	chr3:52287293-52287294
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52286679..52290007-chr3:52290235..52292692,3	K562	blood:
2	chr3:52286492..52290913-chr3:52310452..52313639,5	K562	blood:
3	chr3:52282888..52285793-chr3:52286904..52289881,4	K562	blood:
4	chr3:52280415..52283175-chr3:52286426..52288417,3	MCF-7	breast:
5	chr3:52278277..52281486-chr3:52282865..52288389,9	K562	blood:

Variant related genes	Relation type
ENSG00000164088	Chromatin interaction
ENSG00000164091	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1060330	0.95[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs11712164	0.81[CHB][hapmap]
rs11717383	0.95[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs13094687	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs1546737	1.00[CEU][hapmap];0.90[GIH][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes]
rs2267847	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2272088	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs2276834	0.83[ASN][1000 genomes]
rs34228726	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs353547	0.85[CHB][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs3844291	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3852063	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3852064	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs411457	0.81[CHB][hapmap]
rs57615517	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57630131	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59565798	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs610060	0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap]
rs6445358	0.95[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs730050	0.85[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap]
rs7614727	0.95[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs7618915	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7622851	0.86[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs7629072	0.85[ASN][1000 genomes]
rs7641255	0.80[LWK][hapmap]
rs9311474	0.82[ASN][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	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
3	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
7	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
8	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
9	nsv876788	chr3:52247110-52367932	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
10	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
11	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs34569561	TMEM110	cis	parietal	SCAN
rs34569561	SPCS1	cis	parietal	SCAN
rs34569561	ITIH4	cis	cerebellum	SCAN
rs34569561	GNL3	cis	cerebellum	SCAN
rs34569561	GNL3	cis	parietal	SCAN
rs34569561	NT5DC2	cis	parietal	SCAN
rs34569561	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs34569561	ITIH4	cis	parietal	SCAN
rs34569561	NT5DC2	cis	lymphoblastoid	seeQTL
rs34569561	GLT8D1	cis	lymphoblastoid	seeQTL
rs34569561	NEK4	cis	parietal	SCAN
rs34569561	PRKCD	cis	parietal	SCAN
rs34569561	CACNA2D3	cis	parietal	SCAN
rs34569561	NEK4	cis	cerebellum	SCAN
rs34569561	RBM6	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52279600-52287400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:52280200-52287600	Weak transcription	HMEC	breast
3	chr3:52280200-52287800	Weak transcription	Small Intestine	intestine
4	chr3:52280200-52290000	Weak transcription	Ovary	ovary
5	chr3:52280400-52291200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:52280600-52287600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:52280600-52288200	Weak transcription	Fetal Kidney	kidney
8	chr3:52280600-52290800	Weak transcription	Psoas Muscle	Psoas
9	chr3:52280600-52292400	Weak transcription	Fetal Heart	heart
10	chr3:52280800-52287400	Weak transcription	K562	blood
11	chr3:52280800-52292600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr3:52281000-52291800	Strong transcription	Fetal Intestine Small	intestine
13	chr3:52281200-52287800	Strong transcription	Fetal Stomach	stomach
14	chr3:52281400-52287600	Strong transcription	Fetal Brain Female	brain
15	chr3:52281600-52287400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:52281600-52287400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:52281600-52287400	Weak transcription	HepG2	liver
18	chr3:52281800-52287400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:52281800-52288200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
20	chr3:52281800-52303400	Weak transcription	Right Atrium	heart
21	chr3:52282000-52287600	Strong transcription	Adipose Nuclei	Adipose
22	chr3:52282000-52298800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:52282000-52299400	Strong transcription	Liver	Liver
24	chr3:52282200-52287400	Strong transcription	Stomach Smooth Muscle	stomach
25	chr3:52282200-52287600	Strong transcription	Brain Anterior Caudate	brain
26	chr3:52282200-52287600	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr3:52282200-52293200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr3:52282200-52303000	Strong transcription	Fetal Lung	lung
29	chr3:52282200-52310000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr3:52282400-52297200	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr3:52282400-52309600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:52282600-52289400	Weak transcription	Fetal Brain Male	brain
33	chr3:52282600-52304000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:52282600-52308200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:52282800-52287600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr3:52282800-52288000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
37	chr3:52282800-52303800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:52282800-52305000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:52283000-52287400	Strong transcription	Fetal Muscle Leg	muscle
40	chr3:52283000-52287800	Strong transcription	Fetal Intestine Large	intestine
41	chr3:52283000-52306000	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr3:52283200-52287400	Strong transcription	Lung	lung
43	chr3:52283200-52308400	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr3:52283400-52304600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr3:52283400-52305400	Strong transcription	Brain Germinal Matrix	brain
46	chr3:52283600-52308800	Strong transcription	Fetal Muscle Trunk	muscle
47	chr3:52283800-52287400	Weak transcription	Aorta	Aorta
48	chr3:52283800-52287600	Strong transcription	Brain Cingulate Gyrus	brain
49	chr3:52283800-52309600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr3:52284000-52287400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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