Variant report

Variant	rs6537749
Chromosome Location	chr1:113218503-113218504
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:113005689..113009641-chr1:113216362..113218803,3	MCF-7	breast:
2	chr1:113215712..113221627-chr1:113253708..113259381,5	MCF-7	breast:
3	chr1:113158395..113164969-chr1:113214433..113222934,24	MCF-7	breast:
4	chr1:113215800..113219074-chr1:113254460..113258669,6	MCF-7	breast:
5	chr1:113175098..113177937-chr1:113216084..113219096,3	K562	blood:
6	chr1:113215224..113219998-chr1:113238829..113244717,20	MCF-7	breast:
7	chr1:113166898..113170034-chr1:113215847..113218530,3	K562	blood:
8	chr1:113161304..113162413-chr1:113217336..113218542,3	Hela-S3	cervix:
9	chr1:113217617..113223835-chr1:113226384..113230990,8	MCF-7	breast:
10	chr1:113160799..113166409-chr1:113215716..113220433,9	K562	blood:
11	chr1:113214002..113222947-chr1:113236890..113251579,47	MCF-7	breast:
12	chr1:113214590..113222957-chr1:113244863..113253590,39	MCF-7	breast:
13	chr1:113157097..113164348-chr1:113214570..113220795,12	MCF-7	breast:
14	chr1:113214866..113222565-chr1:113237012..113253952,54	K562	blood:

No data

Variant related genes	Relation type
ENSG00000155366	Chromatin interaction
ENSG00000007341	Chromatin interaction
ENSG00000271810	Chromatin interaction
ENSG00000261595	Chromatin interaction
ENSG00000155363	Chromatin interaction
ENSG00000155367	Chromatin interaction
ENSG00000225075	Chromatin interaction
ENSG00000252750	Chromatin interaction
ENSG00000134245	Chromatin interaction
ENSG00000235299	Chromatin interaction
ENSG00000116489	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10745330	0.82[CEU][hapmap];0.81[GIH][hapmap];0.82[TSI][hapmap]
rs10776755	1.00[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.80[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap]
rs10776757	0.92[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap]
rs10857963	0.82[CEU][hapmap]
rs1110043	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11584092	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12042407	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12046208	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12126277	0.82[CEU][hapmap]
rs2932532	0.82[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs2932536	0.82[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs2999154	0.83[GIH][hapmap];0.89[TSI][hapmap]
rs2999155	0.82[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs2999156	0.93[GIH][hapmap]
rs3013439	0.80[CEU][hapmap]
rs3013440	0.82[CEU][hapmap]
rs351372	0.81[GIH][hapmap];0.80[TSI][hapmap]
rs4838959	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs4839254	0.89[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap]
rs55675817	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6537748	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6666579	0.82[CEU][hapmap];0.81[GIH][hapmap];0.87[TSI][hapmap]
rs6682737	0.82[CEU][hapmap];0.81[GIH][hapmap];0.89[TSI][hapmap]
rs6700673	0.82[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs72699100	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7415820	0.82[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs7513716	0.82[CEU][hapmap]
rs7522288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7544663	0.82[CEU][hapmap];0.81[GIH][hapmap];0.89[TSI][hapmap]
rs7554916	0.81[GIH][hapmap];0.87[TSI][hapmap]
rs902289	0.82[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs937053	0.97[ASN][1000 genomes]
rs9429486	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][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	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
5	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
6	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs6537749	ST7L	cis	lymphoblastoid	seeQTL
rs6537749	CAPZA1	Cis_1M	lymphoblastoid	RTeQTL
rs6537749	CTTNBP2NL	cis	parietal	SCAN
rs6537749	WNT2B	cis	parietal	SCAN
rs6537749	ST7L	cis	parietal	SCAN
rs6537749	C1orf162	cis	parietal	SCAN
rs6537749	ST7L	cis	multi-tissue	Pritchard
rs6537749	SYCP1	cis	parietal	SCAN
rs6537749	ST7L	cis	Artery Tibial	GTEx
rs6537749	ST7L	cis	Thyroid	GTEx
rs6537749	ST7L	cis	lung	GTEx
rs6537749	ST7L	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113216600-113218600	Active TSS	Ovary	ovary
2	chr1:113216600-113218600	Active TSS	Right Ventricle	heart
3	chr1:113216800-113218600	Active TSS	Fetal Kidney	kidney
4	chr1:113216800-113218600	Active TSS	Lung	lung
5	chr1:113216800-113218800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:113217000-113218600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:113217000-113218600	Active TSS	Pancreas	Pancrea
8	chr1:113217000-113218600	Active TSS	Small Intestine	intestine
9	chr1:113217000-113218800	Active TSS	Left Ventricle	heart
10	chr1:113217200-113218600	Active TSS	Fetal Brain Female	brain
11	chr1:113217200-113218800	Active TSS	Fetal Muscle Trunk	muscle
12	chr1:113217200-113219000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:113217600-113219200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:113217800-113218600	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr1:113217800-113218600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:113218000-113218600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
17	chr1:113218000-113218600	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr1:113218000-113218600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:113218000-113218600	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr1:113218000-113218600	Flanking Active TSS	Stomach Smooth Muscle	stomach
21	chr1:113218000-113218800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr1:113218000-113218800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
23	chr1:113218000-113218800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:113218000-113218800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
25	chr1:113218000-113218800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:113218000-113218800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
27	chr1:113218000-113218800	Flanking Active TSS	NHEK	skin
28	chr1:113218000-113219000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr1:113218200-113218600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
30	chr1:113218200-113218600	Flanking Bivalent TSS/Enh	H9 Cell Line	embryonic stem cell
31	chr1:113218200-113218600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:113218200-113218600	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:113218200-113218600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:113218200-113218600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:113218200-113218600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:113218200-113218600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
37	chr1:113218200-113218600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
38	chr1:113218200-113218600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr1:113218200-113218600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:113218200-113218600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:113218200-113218600	Flanking Active TSS	Brain Angular Gyrus	brain
42	chr1:113218200-113218600	Flanking Active TSS	Brain Substantia Nigra	brain
43	chr1:113218200-113218600	Flanking Active TSS	Colonic Mucosa	Colon
44	chr1:113218200-113218600	Flanking Active TSS	Fetal Brain Male	brain
45	chr1:113218200-113218600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
46	chr1:113218200-113218600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr1:113218200-113218600	Flanking Active TSS	Thymus	Thymus
48	chr1:113218200-113218600	Flanking Active TSS	HSMMtube	muscle
49	chr1:113218200-113218600	Flanking Active TSS	K562	blood
50	chr1:113218200-113218600	Flanking Active TSS	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links