Variant report

Variant	rs2523500
Chromosome Location	chr6:31518354-31518355
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RELA	chr6:31517993-31518528	GM12891	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31517592..31522537-chr6:31564964..31567939,4	MCF-7	breast:
2	chr6:31464287..31467209-chr6:31516370..31519006,2	K562	blood:
3	chr6:31516324..31518806-chr6:31543079..31545738,3	MCF-7	breast:
4	chr6:31516732..31519284-chr6:31611132..31613587,2	K562	blood:
5	chr6:31513053..31519210-chr6:31585987..31595406,29	K562	blood:
6	chr6:31513771..31519008-chr6:31582734..31585702,4	K562	blood:
7	chr6:31516810..31518373-chr6:31543320..31545185,2	K562	blood:
8	chr6:31518175..31519881-chr6:31566042..31567461,7	MCF-7	breast:
9	chr6:31509907..31511737-chr6:31518238..31520008,2	MCF-7	breast:
10	chr6:31515650..31517659-chr6:31517852..31520397,2	MCF-7	breast:

No data

Variant related genes	Relation type
ATP6V1G2	TF binding region
ATP6V1G2-DDX39B	TF binding region
ENSG00000198563	Chromatin interaction
ENSG00000213760	Chromatin interaction
ENSG00000204516	Chromatin interaction
ENSG00000234006	Chromatin interaction
ENSG00000201680	Chromatin interaction
ENSG00000204463	Chromatin interaction
ENSG00000204469	Chromatin interaction
ENSG00000200816	Chromatin interaction
ENSG00000232810	Chromatin interaction
ENSG00000204472	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1121800	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2071590	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2239704	0.89[AMR][1000 genomes]
rs2516390	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2516391	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2516401	0.80[AFR][1000 genomes]
rs2516479	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2844483	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2844484	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2844485	0.80[AMR][1000 genomes]
rs2844486	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2857602	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2857710	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs3094595	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs3135042	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3135043	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs746868	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs928815	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
2	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
3	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases
4	nsv601609	chr6:31280101-31799786	Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
5	nsv601610	chr6:31280101-31960770	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	370 gene(s)	inside rSNPs	diseases
6	nsv601628	chr6:31280327-31990098	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
7	nsv601629	chr6:31280327-31996185	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
8	nsv601630	chr6:31280327-32011317	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS 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	378 gene(s)	inside rSNPs	diseases
9	nsv601631	chr6:31280327-32017540	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer 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	378 gene(s)	inside rSNPs	diseases
10	nsv1023939	chr6:31325961-32026747	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
11	nsv538188	chr6:31325961-32026747	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
12	nsv1018463	chr6:31337336-31525275	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS 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	104 gene(s)	inside rSNPs	diseases
13	nsv538189	chr6:31337336-31525275	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	104 gene(s)	inside rSNPs	diseases
14	nsv432868	chr6:31338844-31721033	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	250 gene(s)	inside rSNPs	diseases
15	esv2757162	chr6:31353329-31542308	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	99 gene(s)	inside rSNPs	diseases
16	nsv1021747	chr6:31386219-31907266	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	330 gene(s)	inside rSNPs	diseases
17	nsv432877	chr6:31412961-31528690	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
18	nsv830627	chr6:31496214-31659950	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
19	nsv470809	chr6:31496915-31544189	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	76 gene(s)	inside rSNPs	diseases
20	nsv884417	chr6:31515078-31525354	Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2523500	HIST1H1B	cis	cerebellum	SCAN
rs2523500	HLA-DRB5	cis	parietal	SCAN
rs2523500	HLA-F	cis	multi-tissue	Pritchard
rs2523500	XXbac-BPG248L24.12	cis	Whole Blood	GTEx
rs2523500	HLA-DRB5	cis	multi-tissue	Pritchard
rs2523500	DEF6	cis	parietal	SCAN
rs2523500	BAT1	cis	multi-tissue	Pritchard
rs2523500	HIST1H3I	cis	cerebellum	SCAN
rs2523500	LST1	cis	lymphoblastoid	seeQTL
rs2523500	HLA-DRB5	cis	lymphoblastoid	GTEx
rs2523500	LST1	cis	multi-tissue	Pritchard
rs2523500	HLA-C	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31515600-31525400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr6:31515600-31525600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:31516000-31526400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr6:31516000-31535800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr6:31516200-31519000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr6:31516200-31519200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr6:31516200-31522400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr6:31516200-31525800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr6:31516400-31518400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:31516400-31518400	Weak transcription	Colonic Mucosa	Colon
11	chr6:31516400-31518600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:31516400-31518600	Weak transcription	Lung	lung
13	chr6:31516400-31518800	Weak transcription	Aorta	Aorta
14	chr6:31516400-31518800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:31516400-31519000	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr6:31516400-31519000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr6:31516400-31519000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr6:31516400-31519000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr6:31516400-31519400	Strong transcription	Fetal Muscle Trunk	muscle
20	chr6:31516400-31522000	Weak transcription	Esophagus	oesophagus
21	chr6:31516400-31522800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:31516400-31523600	Weak transcription	Primary hematopoietic stem cells	blood
23	chr6:31516400-31523800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:31516400-31523800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr6:31516400-31523800	Weak transcription	Ovary	ovary
26	chr6:31516400-31523800	Weak transcription	Pancreas	Pancrea
27	chr6:31516400-31525400	Weak transcription	Right Atrium	heart
28	chr6:31516400-31526200	Weak transcription	Small Intestine	intestine
29	chr6:31516400-31526200	Weak transcription	NH-A	brain
30	chr6:31516400-31526200	Weak transcription	NHDF-Ad	bronchial
31	chr6:31516400-31526400	Weak transcription	A549	lung
32	chr6:31516400-31526600	Weak transcription	Psoas Muscle	Psoas
33	chr6:31516400-31527200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:31516400-31533200	Weak transcription	Fetal Brain Male	brain
35	chr6:31516600-31518800	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr6:31516600-31518800	Weak transcription	Gastric	stomach
37	chr6:31516600-31519000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr6:31516600-31519200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:31516600-31519200	Strong transcription	Thymus	Thymus
40	chr6:31516600-31521000	Weak transcription	HSMMtube	muscle
41	chr6:31516600-31521800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr6:31516600-31522200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr6:31516600-31522400	Strong transcription	Fetal Intestine Small	intestine
44	chr6:31516600-31523800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr6:31516600-31523800	Weak transcription	Spleen	Spleen
46	chr6:31516600-31525200	Strong transcription	Fetal Muscle Leg	muscle
47	chr6:31516600-31529200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr6:31516800-31518800	Weak transcription	Rectal Smooth Muscle	rectum
49	chr6:31516800-31518800	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr6:31516800-31519000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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