Variant report

Variant	rs2370142
Chromosome Location	chr11:67348642-67348643
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:67275111..67277928-chr11:67348479..67351408,2	MCF-7	breast:
2	chr11:67348020..67353194-chr11:67379787..67385803,14	K562	blood:
3	chr11:67347575..67355744-chr11:67372717..67376912,13	K562	blood:
4	chr11:67348370..67350367-chr11:67374395..67376609,2	MCF-7	breast:
5	chr11:67347249..67355748-chr11:67372717..67377095,16	K562	blood:
6	chr11:67344360..67352769-chr11:67395394..67400721,12	K562	blood:

Variant related genes	Relation type
ENSG00000255119	Chromatin interaction
ENSG00000167799	Chromatin interaction
ENSG00000167797	Chromatin interaction
ENSG00000231793	Chromatin interaction
ENSG00000167792	Chromatin interaction
ENSG00000184224	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1079719	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10896181	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11603735	0.84[ASN][1000 genomes]
rs11605586	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17593068	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1871042	0.85[ASN][1000 genomes]
rs2370141	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2370143	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36211089	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4930436	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55854833	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58046082	0.86[EUR][1000 genomes]
rs597297	0.80[ASN][1000 genomes]
rs6591249	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6591251	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6591252	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6591253	0.84[ASN][1000 genomes]
rs6591254	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6591255	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6591256	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6591258	0.85[ASN][1000 genomes]
rs7103713	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7106423	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7106675	0.89[EUR][1000 genomes]
rs7108426	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs749174	0.84[ASN][1000 genomes]
rs762803	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7927657	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7940813	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7941395	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7941648	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7945035	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7945927	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7948478	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7948823	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7948911	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7949394	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7949587	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7952081	0.89[EUR][1000 genomes]
rs947895	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531397	chr11:66653381-67465721	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1043037	chr11:67027193-67357425	Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
3	nsv897801	chr11:67033076-67432479	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
4	nsv897807	chr11:67155210-67414492	Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
5	nsv897808	chr11:67155210-67419855	Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
6	nsv534229	chr11:67164667-67411909	Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
7	esv2422195	chr11:67234322-67626901	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	146 gene(s)	inside rSNPs	diseases
8	nsv1041988	chr11:67319916-67749246	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
9	nsv897814	chr11:67339949-67460529	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
10	nsv1050463	chr11:67343421-67717338	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
11	nsv1038189	chr11:67345320-67749246	Transcr. at gene 5' and 3' Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
12	nsv1047236	chr11:67345320-67764068	Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
13	nsv555268	chr11:67346743-67752972	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
14	nsv1036101	chr11:67346813-67828351	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
15	nsv541079	chr11:67346813-67828351	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
16	nsv897815	chr11:67347595-67408791	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer 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 target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2370142	PTPRCAP	cis	Nerve Tibial	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:67344400-67350600	Enhancers	Stomach Mucosa	stomach
2	chr11:67345600-67350200	Enhancers	Fetal Intestine Small	intestine
3	chr11:67346000-67348800	Weak transcription	Placenta	Placenta
4	chr11:67346800-67350600	Enhancers	Pancreas	Pancrea
5	chr11:67346800-67351000	Enhancers	Liver	Liver
6	chr11:67347200-67348800	Enhancers	A549	lung
7	chr11:67347200-67350200	Weak transcription	Right Ventricle	heart
8	chr11:67347400-67349000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr11:67347400-67349600	Weak transcription	Primary T cells from cord blood	blood
10	chr11:67347400-67349800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr11:67347400-67349800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr11:67347400-67350000	Enhancers	Fetal Kidney	kidney
13	chr11:67347400-67350000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr11:67347400-67350200	Weak transcription	Colonic Mucosa	Colon
15	chr11:67347400-67350400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr11:67347400-67351200	Weak transcription	Spleen	Spleen
17	chr11:67347600-67348800	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr11:67347600-67349000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr11:67347600-67349000	Weak transcription	Hela-S3	cervix
20	chr11:67347600-67349200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr11:67347600-67349600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr11:67347600-67349600	Weak transcription	Primary B cells from peripheral blood	blood
23	chr11:67347600-67349600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr11:67347600-67349600	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr11:67347600-67349800	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr11:67347600-67349800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr11:67347600-67349800	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr11:67347600-67350000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr11:67347600-67350000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr11:67347600-67350000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr11:67347600-67350000	Weak transcription	HMEC	breast
32	chr11:67347600-67350200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr11:67347600-67350200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr11:67347600-67350400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr11:67347600-67350400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr11:67347600-67350400	Enhancers	HepG2	liver
37	chr11:67347600-67350400	Weak transcription	HSMM	muscle
38	chr11:67347800-67348800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr11:67347800-67349000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr11:67347800-67349200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr11:67347800-67350000	Weak transcription	Small Intestine	intestine
42	chr11:67347800-67350800	Weak transcription	Gastric	stomach
43	chr11:67348000-67349600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr11:67348000-67350000	Weak transcription	Lung	lung
45	chr11:67348200-67348800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr11:67348200-67350000	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr11:67348400-67348800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr11:67348400-67349200	Weak transcription	K562	blood
49	chr11:67348400-67350400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr11:67348400-67350800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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