Variant report

Variant	rs2535627
Chromosome Location	chr3:52845105-52845106
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52804079..52807046-chr3:52844377..52847096,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ITIH4-2	chr3:52844728-52846754	NONHSAT089960

Variant related genes	Relation type
ENSG00000114904	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1042779	0.83[CHB][hapmap]
rs11918800	0.90[YRI][hapmap]
rs11922961	0.90[YRI][hapmap]
rs2019065	0.83[CHB][hapmap]
rs2071042	0.90[YRI][hapmap]
rs2071044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2071506	0.83[CHB][hapmap]
rs2239551	0.82[CHB][hapmap]
rs2240915	0.90[YRI][hapmap]
rs2240917	0.84[YRI][hapmap]
rs2256332	0.81[YRI][hapmap]
rs2302417	0.85[EUR][1000 genomes]
rs2535629	0.83[CHB][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap]
rs2535633	0.90[YRI][hapmap]
rs2710323	0.84[CEU][hapmap];0.87[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs3617	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4481150	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.84[MKK][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs736408	0.87[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs9324	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
3	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1010761	chr3:52804547-52851258	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	esv1810629	chr3:52817031-52869635	Weak transcription Active TSS Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv876797	chr3:52817675-52873984	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Schizophrenia	25056061	GWAS catalog

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2535627	FLJ12442	cis	multi-tissue	Pritchard
rs2535627	ITIH4	cis	multi-tissue	Pritchard
rs2535627	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs2535627	NT5DC2	cis	multi-tissue	Pritchard
rs2535627	ITIH4	cis	Lymphoblastoid	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52836800-52851600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:52836800-52851800	Weak transcription	Pancreas	Pancrea
3	chr3:52838000-52847200	Enhancers	Fetal Thymus	thymus
4	chr3:52838400-52852000	Weak transcription	Spleen	Spleen
5	chr3:52841600-52850600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:52842000-52846000	Enhancers	Thymus	Thymus
7	chr3:52842800-52845600	Enhancers	HepG2	liver
8	chr3:52843800-52846600	Weak transcription	Fetal Stomach	stomach
9	chr3:52844000-52847200	Enhancers	Liver	Liver
10	chr3:52844000-52847200	Weak transcription	Fetal Muscle Leg	muscle
11	chr3:52844000-52854000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr3:52844200-52856600	Weak transcription	Primary T cells from cord blood	blood
13	chr3:52844400-52857200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:52844600-52851600	Weak transcription	Fetal Muscle Trunk	muscle
15	chr3:52844600-52851800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:52844600-52856800	Weak transcription	Fetal Intestine Small	intestine
17	chr3:52844600-52857600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:52845000-52845400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr3:52845000-52845400	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr3:52845000-52845600	Enhancers	Skeletal Muscle Male	skeletal muscle

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