Variant report

Variant	rs2662256
Chromosome Location	chr5:98131350-98131351
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:98129808..98132282-chr5:98134081..98135788,2	K562	blood:
2	chr5:98123018..98126275-chr5:98130087..98132367,4	MCF-7	breast:
3	chr5:98105450..98112138-chr5:98128603..98138411,14	MCF-7	breast:
4	chr5:98124398..98126468-chr5:98128299..98131960,3	MCF-7	breast:
5	chr5:98126420..98128371-chr5:98130230..98131989,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000246763	Chromatin interaction
ENSG00000174136	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10515283	1.00[ASN][1000 genomes]
rs150935	0.83[YRI][hapmap]
rs161729	1.00[YRI][hapmap]
rs161732	0.82[YRI][hapmap]
rs161739	0.83[YRI][hapmap]
rs161746	0.83[YRI][hapmap]
rs161750	0.83[YRI][hapmap]
rs161940	1.00[YRI][hapmap]
rs1828168	1.00[ASN][1000 genomes]
rs2545677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545728	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545729	0.91[EUR][1000 genomes]
rs2545735	0.83[YRI][hapmap]
rs2578576	0.83[YRI][hapmap]
rs2578577	0.83[YRI][hapmap]
rs2617508	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2617512	0.90[EUR][1000 genomes]
rs2617515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2662255	0.91[EUR][1000 genomes]
rs2662259	0.91[EUR][1000 genomes]
rs2662260	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2662261	0.91[EUR][1000 genomes]
rs2859485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325195	0.83[YRI][hapmap]
rs325199	0.83[YRI][hapmap]
rs325203	1.00[YRI][hapmap]
rs325204	1.00[YRI][hapmap]
rs325208	0.83[YRI][hapmap]
rs331542	0.83[YRI][hapmap]
rs34498	0.82[YRI][hapmap]
rs72773677	1.00[ASN][1000 genomes]
rs72773692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72773694	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882414	chr5:98063710-98193164	Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2662256	RGMB	cis	normal skin	skin_eQTL
rs2662256	RGMB	Cis_1M	lymphoblastoid	RTeQTL
rs2662256	RGMB	cis	uninvolved skin	skin_eQTL
rs2662256	RGMB	cis	lesional skin	skin_eQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98111000-98131800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:98111600-98131800	Weak transcription	Placenta	Placenta
3	chr5:98112000-98135800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr5:98114800-98131400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr5:98117600-98132200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr5:98118400-98131800	Weak transcription	A549	lung
7	chr5:98122200-98132000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr5:98123000-98132400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr5:98123800-98132000	Weak transcription	Primary T cells from cord blood	blood
10	chr5:98123800-98136800	Weak transcription	Fetal Brain Male	brain
11	chr5:98123800-98140600	Weak transcription	Brain Substantia Nigra	brain
12	chr5:98124000-98132000	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr5:98124000-98132000	Weak transcription	Fetal Lung	lung
14	chr5:98125200-98132000	Genic enhancers	NHDF-Ad	bronchial
15	chr5:98125600-98132000	Weak transcription	Stomach Mucosa	stomach
16	chr5:98127400-98131600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:98127600-98131600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr5:98127600-98131800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr5:98127600-98131800	Weak transcription	Fetal Kidney	kidney
20	chr5:98127800-98131800	Weak transcription	Colon Smooth Muscle	Colon
21	chr5:98128600-98131400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr5:98129000-98131400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr5:98129200-98131600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr5:98129200-98132200	Weak transcription	Hela-S3	cervix
25	chr5:98129400-98131400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr5:98129400-98131600	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr5:98129400-98131600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr5:98129400-98131600	Weak transcription	Left Ventricle	heart
29	chr5:98129400-98131600	Weak transcription	Pancreas	Pancrea
30	chr5:98129400-98131800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr5:98129400-98131800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr5:98129400-98131800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr5:98129400-98132000	Weak transcription	Spleen	Spleen
34	chr5:98129400-98132200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr5:98129400-98132200	Weak transcription	HMEC	breast
36	chr5:98129400-98132600	Weak transcription	Primary B cells from peripheral blood	blood
37	chr5:98129400-98132800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr5:98129400-98132800	Weak transcription	Brain Hippocampus Middle	brain
39	chr5:98129400-98141200	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr5:98129600-98136000	Weak transcription	Esophagus	oesophagus
41	chr5:98129800-98131800	Weak transcription	Small Intestine	intestine
42	chr5:98130000-98131400	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr5:98130000-98131600	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr5:98130000-98131600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr5:98130000-98131600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr5:98130000-98131600	Weak transcription	Brain Anterior Caudate	brain
47	chr5:98130000-98131600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr5:98130000-98131600	Weak transcription	HepG2	liver
49	chr5:98130000-98131800	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr5:98130000-98131800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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