Variant report

Variant	rs62144417
Chromosome Location	chr2:87303060-87303061
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:87281176..87283798-chr2:87302577..87304633,2	MCF-7	breast:
2	chr2:86789024..86791664-chr2:87302659..87304185,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228363	Chromatin interaction
ENSG00000115561	Chromatin interaction
ENSG00000266931	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs3890849	1.00[AMR][1000 genomes]
rs56704278	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:33 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532319	chr2:87024867-88005418	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv1800069	chr2:87056027-87885905	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1010107	chr2:87105444-88052318	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
4	nsv519198	chr2:87108211-87771196	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
5	esv33176	chr2:87122115-87325330	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv1803562	chr2:87126250-88038663	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
7	nsv997663	chr2:87126250-88052318	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
8	esv2757815	chr2:87155912-88042080	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
9	esv1796172	chr2:87245762-88042080	Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
10	nsv428398	chr2:87245762-88042080	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
11	esv1801752	chr2:87245762-88123177	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
12	nsv1002590	chr2:87250484-87960588	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
13	nsv1011527	chr2:87250484-88052318	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
14	nsv10065	chr2:87255641-87345941	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
15	nsv1000885	chr2:87260341-87849159	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
16	nsv1003162	chr2:87260341-87960588	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
17	nsv1014950	chr2:87260341-88024655	Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
18	nsv874476	chr2:87262856-87424779	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
19	nsv874477	chr2:87262856-87453247	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
20	nsv1007205	chr2:87278884-87960588	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
21	nsv1002598	chr2:87278884-88046609	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
22	nsv1011714	chr2:87278884-88052318	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
23	nsv874478	chr2:87281373-87361162	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
24	nsv874479	chr2:87281373-87424779	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
25	nsv874480	chr2:87281373-87432615	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
26	nsv874481	chr2:87281373-87522277	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
27	nsv961805	chr2:87292841-87345428	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
28	nsv874482	chr2:87293789-87410663	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
29	nsv916253	chr2:87295670-88005429	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
30	nsv870024	chr2:87295735-88187783	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
31	nsv1003146	chr2:87302095-87960588	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
32	nsv1006012	chr2:87302095-88024655	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
33	esv1795912	chr2:87302540-87590895	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs62144417	LOC285074	Cis_1M	lymphoblastoid	RTeQTL
rs62144417	PLGLA1///PLGLB1///PLGLB2	N/A	lymphoblastoid	RTeQTL
rs62144417	PLGLB1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:87301000-87304400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr2:87301000-87304400	Active TSS	Fetal Intestine Small	intestine
3	chr2:87302000-87303400	Active TSS	Fetal Lung	lung
4	chr2:87302000-87304000	Active TSS	Primary hematopoietic stem cells	blood
5	chr2:87302000-87304200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:87302000-87304200	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr2:87302000-87304200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr2:87302000-87304200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr2:87302000-87304200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
10	chr2:87302000-87304200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr2:87302000-87304200	Active TSS	Brain Substantia Nigra	brain
12	chr2:87302000-87304200	Active TSS	Fetal Kidney	kidney
13	chr2:87302000-87304200	Active TSS	GM12878-XiMat	blood
14	chr2:87302000-87304200	Active TSS	Hela-S3	cervix
15	chr2:87302000-87304200	Active TSS	K562	blood
16	chr2:87302000-87304200	Active TSS	NHDF-Ad	bronchial
17	chr2:87302000-87304200	Active TSS	NHLF	lung
18	chr2:87302000-87304400	Active TSS	H1 Cell Line	embryonic stem cell
19	chr2:87302000-87304400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:87302000-87304400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:87302000-87304400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr2:87302000-87304400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr2:87302000-87304400	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr2:87302000-87304400	Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr2:87302000-87304400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:87302000-87304400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr2:87302000-87304400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:87302000-87304400	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr2:87302000-87304400	Active TSS	Primary hematopoietic stem cells short term culture	blood
30	chr2:87302000-87304400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr2:87302000-87304400	Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr2:87302000-87304400	Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr2:87302000-87304400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:87302000-87304400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr2:87302000-87304400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr2:87302000-87304400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr2:87302000-87304400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr2:87302000-87304400	Active TSS	Brain Angular Gyrus	brain
39	chr2:87302000-87304400	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr2:87302000-87304400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr2:87302000-87304400	Active TSS	Colonic Mucosa	Colon
42	chr2:87302000-87304400	Active TSS	Duodenum Mucosa	Duodenum
43	chr2:87302000-87304400	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr2:87302000-87304400	Active TSS	Esophagus	oesophagus
45	chr2:87302000-87304400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr2:87302000-87304400	Active TSS	Fetal Intestine Large	intestine
47	chr2:87302000-87304400	Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr2:87302000-87304400	Active TSS	Fetal Muscle Trunk	muscle
49	chr2:87302000-87304400	Active TSS	Placenta	Placenta
50	chr2:87302000-87304400	Active TSS	Fetal Stomach	stomach

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