Variant report

Variant	rs1975535
Chromosome Location	chr2:113942903-113942904
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:66218804..66221385-chr2:113942037..113943600,2	MCF-7	breast:
2	chr2:113941477..113944460-chr2:113951684..113956081,4	K562	blood:
3	chr2:113914770..113916591-chr2:113941477..113943871,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IL1RN-3	chr2:113942707-113943178	expReg_chr2_8717_+

Variant related genes	Relation type
ENSG00000125637	Chromatin interaction
ENSG00000241749	Chromatin interaction
ENSG00000149948	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12711762	0.83[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs12711765	0.89[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2241976	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3748914	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3791337	0.81[EUR][1000 genomes]
rs4848316	0.93[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4849163	0.82[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs4849166	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4849167	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4849168	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6737029	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6750127	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6760120	0.88[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.87[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6761202	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7595962	0.84[JPT][hapmap];0.85[ASN][1000 genomes]

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	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv582711	chr2:113895516-113984503	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv582712	chr2:113932431-113985170	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised 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	14 gene(s)	inside rSNPs	diseases
4	nsv874897	chr2:113935407-113944762	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv874898	chr2:113935407-113954247	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv874899	chr2:113935407-113962071	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1975535	PSD4	cis	Thyroid	GTEx
rs1975535	PSD4	cis	lung	GTEx
rs1975535	PSD4	cis	Stomach	GTEx
rs1975535	PSD4	cis	Nerve Tibial	GTEx
rs1975535	PSD4	cis	Whole Blood	GTEx
rs1975535	PSD4	cis	Skin Sun Exposed Lower leg	GTEx
rs1975535	PSD4	cis	Esophagus Muscularis	GTEx
rs1975535	PSD4	cis	Esophagus Mucosa	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113923000-113951800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:113923000-113956000	Weak transcription	HMEC	breast
3	chr2:113934200-113949000	Genic enhancers	Primary B cells from peripheral blood	blood
4	chr2:113934200-113956200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:113934400-113948600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:113934600-113946400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr2:113938000-113945000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:113938800-113945800	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr2:113939000-113944200	Genic enhancers	Spleen	Spleen
10	chr2:113939000-113944600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:113939200-113945600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr2:113939400-113945200	Strong transcription	Fetal Stomach	stomach
13	chr2:113939400-113945400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:113939400-113946400	Genic enhancers	Primary T cells fromperipheralblood	blood
15	chr2:113939400-113946800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr2:113939400-113948400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
17	chr2:113939400-113949000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr2:113939400-113956000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr2:113939400-113956400	Weak transcription	Small Intestine	intestine
20	chr2:113939600-113943000	Genic enhancers	Duodenum Mucosa	Duodenum
21	chr2:113939600-113943200	Weak transcription	Adipose Nuclei	Adipose
22	chr2:113939600-113943200	Weak transcription	Fetal Muscle Leg	muscle
23	chr2:113939600-113945600	Strong transcription	K562	blood
24	chr2:113939600-113947800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
25	chr2:113939600-113953800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr2:113939600-113955400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr2:113939600-113956200	Weak transcription	Fetal Lung	lung
28	chr2:113939800-113943000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:113939800-113943200	Weak transcription	Brain Anterior Caudate	brain
30	chr2:113939800-113945000	Genic enhancers	Monocytes-CD14+_RO01746	blood
31	chr2:113939800-113945400	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr2:113939800-113946200	Strong transcription	Thymus	Thymus
33	chr2:113940000-113943400	Weak transcription	Gastric	stomach
34	chr2:113940000-113944200	Genic enhancers	Liver	Liver
35	chr2:113940000-113945600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:113940000-113946800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr2:113940000-113961000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr2:113940400-113950000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr2:113940600-113943400	Weak transcription	Lung	lung
40	chr2:113940600-113945800	Strong transcription	Primary hematopoietic stem cells	blood
41	chr2:113941000-113943000	Genic enhancers	Fetal Intestine Small	intestine
42	chr2:113941000-113944200	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr2:113941000-113944400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr2:113941000-113945200	Genic enhancers	Primary B cells from cord blood	blood
45	chr2:113941000-113950000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr2:113941200-113943200	Weak transcription	Pancreas	Pancrea
47	chr2:113941200-113949800	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr2:113941400-113950000	Weak transcription	Esophagus	oesophagus
49	chr2:113941600-113943600	Enhancers	Placenta	Placenta
50	chr2:113941600-113944000	Weak transcription	Rectal Mucosa Donor 31	rectum

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