Variant report

Variant	rs288253
Chromosome Location	chr2:183609373-183609374
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:183580042..183581600-chr2:183608683..183611229,2	MCF-7	breast:
2	chr2:183598485..183600408-chr2:183608277..183611050,2	MCF-7	breast:
3	chr2:183600722..183602612-chr2:183608045..183610895,3	K562	blood:
4	chr2:183603082..183605652-chr2:183608398..183611324,2	K562	blood:

Variant related genes	Relation type
ENSG00000077232	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1037404	0.80[EUR][1000 genomes]
rs11678585	0.82[EUR][1000 genomes]
rs11901549	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13509	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs167013	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17356762	0.84[CEU][hapmap]
rs184078	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs190830	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs192618	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs208393	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2118591	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs288239	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs288240	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs288241	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs288254	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs288256	0.86[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs288257	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs288258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs288259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs288260	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs288263	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs288264	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs288265	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs288267	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs288268	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs288269	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs288271	0.85[ASN][1000 genomes]
rs288278	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs288280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs288283	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs288285	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs288287	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs288289	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs288291	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs288292	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs288293	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs288294	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs288295	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs288296	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs288299	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs288300	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs288302	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs288303	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs288304	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs288305	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs288306	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs288307	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs288308	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs288309	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs288310	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs288311	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs288312	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs288313	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs288331	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs288332	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs288334	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs288335	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs288336	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs288343	0.82[AFR][1000 genomes]
rs288344	0.84[AFR][1000 genomes]
rs288346	0.84[AFR][1000 genomes]
rs288347	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs288349	0.89[ASN][1000 genomes]
rs3115425	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34818934	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs369573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs384190	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs409343	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs418159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs418474	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs432527	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs438248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs442044	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6727545	0.86[EUR][1000 genomes]
rs73975514	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7588247	0.88[EUR][1000 genomes]
rs825660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs825668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9677291	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9678817	0.80[EUR][1000 genomes]

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	nsv1009882	chr2:183213152-184171519	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2757842	chr2:183437700-183835084	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2759104	chr2:183437700-183835084	Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv2756954	chr2:183528670-183764930	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv875483	chr2:183537399-183657867	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	esv34847	chr2:183537399-183786763	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	esv3693445	chr2:183542825-183725221	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs288253	DNAJC10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:183581600-183609600	Weak transcription	Spleen	Spleen
2	chr2:183581800-183614600	Weak transcription	Right Ventricle	heart
3	chr2:183581800-183622600	Weak transcription	Colonic Mucosa	Colon
4	chr2:183581800-183631000	Weak transcription	Esophagus	oesophagus
5	chr2:183581800-183647600	Weak transcription	Gastric	stomach
6	chr2:183581800-183655600	Weak transcription	Pancreas	Pancrea
7	chr2:183582400-183610000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:183582600-183610600	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr2:183582600-183624400	Weak transcription	Stomach Mucosa	stomach
10	chr2:183582800-183610000	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr2:183582800-183610000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr2:183582800-183614600	Weak transcription	Fetal Brain Male	brain
13	chr2:183584200-183610400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:183584800-183610200	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr2:183584800-183610400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:183584800-183610400	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr2:183588600-183611200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:183588600-183624200	Weak transcription	Small Intestine	intestine
19	chr2:183591400-183610400	Strong transcription	Primary B cells from peripheral blood	blood
20	chr2:183591400-183622600	Weak transcription	Brain Germinal Matrix	brain
21	chr2:183599200-183610400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:183599800-183610400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:183600000-183610400	Strong transcription	HUVEC	blood vessel
24	chr2:183600200-183610400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr2:183600400-183609600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:183600800-183610400	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr2:183600800-183610400	Strong transcription	NH-A	brain
28	chr2:183601000-183609600	Strong transcription	Primary B cells from cord blood	blood
29	chr2:183601000-183610400	Strong transcription	Osteobl	bone
30	chr2:183601600-183620000	Weak transcription	Colon Smooth Muscle	Colon
31	chr2:183602600-183609400	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr2:183602600-183622600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:183602600-183624200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr2:183603200-183622400	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr2:183604600-183610400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:183604600-183610400	Strong transcription	Placenta	Placenta
37	chr2:183605000-183610000	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr2:183605000-183610400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:183605000-183610400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:183605200-183610400	Strong transcription	Adipose Nuclei	Adipose
41	chr2:183605200-183610400	Strong transcription	Duodenum Mucosa	Duodenum
42	chr2:183605200-183610400	Strong transcription	HMEC	breast
43	chr2:183605200-183610600	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr2:183605200-183610800	Strong transcription	Fetal Intestine Large	intestine
45	chr2:183605400-183610200	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr2:183605400-183610400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr2:183605600-183610200	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr2:183605600-183610400	Strong transcription	Brain Anterior Caudate	brain
49	chr2:183605600-183610600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr2:183605600-183646000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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