Variant report

Variant	rs1554721
Chromosome Location	chr6:36955064-36955065
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:36955049-36955138	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr6:36953632-36955129	K562	blood:	n/a	n/a
3	MYC	chr6:36953758-36955211	K562	blood:	n/a	chr6:36953976-36953985 chr6:36953976-36953985 chr6:36953976-36953985
4	POLR2A	chr6:36955028-36955078	ProgFib	skin:	n/a	n/a
5	POLR2A	chr6:36954808-36955069	GM12878	blood:	n/a	n/a
6	TBL1XR1	chr6:36953650-36955229	K562	blood:	n/a	n/a
7	POLR2A	chr6:36953426-36955258	K562	blood:	n/a	n/a
8	POLR2A	chr6:36953652-36955097	MCF10A-Er-Src	breast:	n/a	n/a
9	MXI1	chr6:36952363-36955399	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr6:36953678-36955323	HepG2	liver:	n/a	n/a
11	POLR2A	chr6:36953520-36955354	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAX	chr6:36953705-36955140	NB4	blood:	n/a	chr6:36953976-36953985 chr6:36953976-36953985 chr6:36953976-36953985
13	TEAD4	chr6:36953495-36955307	K562	blood:	n/a	n/a
14	POLR2A	chr6:36953440-36955247	PFSK-1	brain:	n/a	n/a
15	JUND	chr6:36952199-36955409	SK-N-SH	brain:	n/a	n/a
16	MAX	chr6:36953487-36955236	K562	blood:	n/a	chr6:36953976-36953985 chr6:36953976-36953985 chr6:36953976-36953985
17	POLR2A	chr6:36953547-36955286	Raji	blood:	n/a	n/a
18	MYC	chr6:36953676-36955081	K562	blood:	n/a	chr6:36953976-36953985 chr6:36953976-36953985 chr6:36953976-36953985
19	POLR2A	chr6:36953667-36955141	MCF10A-Er-Src	breast:	n/a	n/a
20	MXI1	chr6:36952134-36955140	IMR90	lung:	n/a	n/a
21	POLR2A	chr6:36953467-36955388	SK-N-MC	brain:	n/a	n/a
22	HCFC1	chr6:36953615-36955076	Hela-S3	cervix:	n/a	n/a
23	SREBP1	chr6:36953627-36955123	GM12878	blood:	n/a	chr6:36953976-36953986 chr6:36953976-36953985 chr6:36953976-36953985 chr6:36953975-36953985
24	CBX3	chr6:36953534-36955213	K562	blood:	n/a	n/a
25	CHD1	chr6:36951658-36955228	IMR90	lung:	n/a	chr6:36953547-36953557 chr6:36952852-36952862 chr6:36954334-36954344
26	POLR2A	chr6:36953334-36955342	HepG2	liver:	n/a	n/a
27	POLR2A	chr6:36953646-36955279	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:36930754..36936310-chr6:36950773..36956274,7	MCF-7	breast:
2	chr6:36952074..36956895-chr6:36967839..36978010,11	MCF-7	breast:
3	chr6:36852278..36855515-chr6:36952430..36957026,4	MCF-7	breast:
4	chr6:36852138..36856054-chr6:36953606..36956862,5	K562	blood:
5	chr6:36889896..36892689-chr6:36954303..36956712,2	MCF-7	breast:
6	chr6:36724390..36726745-chr6:36953555..36956553,2	K562	blood:
7	chr6:36929829..36933522-chr6:36953197..36956380,5	MCF-7	breast:
8	chr6:36936791..36939065-chr6:36954271..36955828,2	MCF-7	breast:
9	chr6:36934908..36939247-chr6:36952489..36955593,6	MCF-7	breast:
10	chr6:36954231..36957100-chr6:36969352..36972549,3	K562	blood:
11	chr6:36838369..36843263-chr6:36951921..36955568,5	MCF-7	breast:
12	chr6:36954227..36956971-chr6:36992385..36994779,2	K562	blood:
13	chr6:36953605..36955180-chr6:37399250..37401093,2	K562	blood:

Variant related genes	Relation type
MTCH1	TF binding region
ENSG00000137200	Chromatin interaction
ENSG00000164530	Chromatin interaction
ENSG00000146192	Chromatin interaction
ENSG00000137168	Chromatin interaction
ENSG00000137409	Chromatin interaction
ENSG00000124772	Chromatin interaction
ENSG00000198663	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12523725	0.89[EUR][1000 genomes]
rs12525363	0.91[CEU][hapmap];0.85[CHB][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13193265	0.91[CEU][hapmap];0.86[CHB][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs16889364	0.87[CHB][hapmap]
rs4711477	0.91[EUR][1000 genomes]
rs4711478	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4714028	0.87[CHB][hapmap];0.82[CHD][hapmap];0.80[ASN][1000 genomes]
rs4714030	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4714031	0.91[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.82[EUR][1000 genomes]
rs56738294	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62406531	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6915207	0.86[CHB][hapmap]
rs708008	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs708010	0.91[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.83[JPT][hapmap];0.89[TSI][hapmap]
rs7739340	0.87[CHB][hapmap]
rs831380	0.91[CHB][hapmap]

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	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv885815	chr6:36915906-36979583	Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv5263	chr6:36941625-36972109	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
5	nsv518386	chr6:36942746-37037670	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv602952	chr6:36951210-36978745	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	esv3404117	chr6:36952499-36955347	Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1554721	TSPO2	cis	cerebellum	SCAN
rs1554721	RPL10A	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36952200-36955200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr6:36952200-36955200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:36952400-36955200	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr6:36952600-36955400	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr6:36952600-36955400	Active TSS	H9 Cell Line	embryonic stem cell
6	chr6:36952600-36955400	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr6:36952600-36955400	Active TSS	Fetal Muscle Trunk	muscle
8	chr6:36952800-36955200	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr6:36954400-36955200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
10	chr6:36954400-36955200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr6:36954400-36955200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:36954400-36955200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr6:36954400-36955200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
14	chr6:36954400-36955200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:36954400-36955200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:36954400-36955200	Flanking Active TSS	Fetal Brain Male	brain
17	chr6:36954400-36955200	Flanking Active TSS	Fetal Thymus	thymus
18	chr6:36954400-36955200	Flanking Active TSS	HMEC	breast
19	chr6:36954400-36955400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:36954400-36955400	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr6:36954400-36955400	Flanking Active TSS	Liver	Liver
22	chr6:36954400-36955400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr6:36954400-36955400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr6:36954400-36955400	Flanking Active TSS	Stomach Smooth Muscle	stomach
25	chr6:36954400-36955400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr6:36954600-36955200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
27	chr6:36954600-36955200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr6:36954600-36955200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr6:36954600-36955200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr6:36954600-36955200	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr6:36954600-36955200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
32	chr6:36954600-36955200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:36954600-36955200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
34	chr6:36954600-36955200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr6:36954600-36955200	Flanking Active TSS	Brain Angular Gyrus	brain
36	chr6:36954600-36955200	Flanking Active TSS	Brain Cingulate Gyrus	brain
37	chr6:36954600-36955200	Flanking Active TSS	Brain Germinal Matrix	brain
38	chr6:36954600-36955200	Flanking Active TSS	Brain Hippocampus Middle	brain
39	chr6:36954600-36955200	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr6:36954600-36955200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
41	chr6:36954600-36955200	Flanking Active TSS	Fetal Intestine Small	intestine
42	chr6:36954600-36955200	Flanking Active TSS	Fetal Muscle Leg	muscle
43	chr6:36954600-36955200	Flanking Active TSS	Fetal Stomach	stomach
44	chr6:36954600-36955200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
45	chr6:36954600-36955200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
46	chr6:36954600-36955200	Flanking Active TSS	Hela-S3	cervix
47	chr6:36954600-36955200	Flanking Active TSS	HSMMtube	muscle
48	chr6:36954600-36955200	Flanking Active TSS	K562	blood
49	chr6:36954600-36955200	Flanking Active TSS	Osteobl	bone
50	chr6:36954600-36955400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links