Variant report

Variant	rs1888983
Chromosome Location	chr10:45462219-45462220
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:39)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:39 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr10:45462200-45462350	RPTEC	kidney:	n/a	n/a
2	POLR2A	chr10:45457577-45464667	GM12878	blood:	n/a	n/a
3	MAZ	chr10:45461180-45462553	GM12878	blood:	n/a	n/a
4	RCOR1	chr10:45461222-45462229	GM12878	blood:	n/a	n/a
5	CTCF	chr10:45462100-45462250	BJ	skin:	n/a	n/a
6	CHD1	chr10:45462030-45462299	GM12878	blood:	n/a	n/a
7	CTCF	chr10:45462160-45462310	HFF-Myc	foreskin:	n/a	n/a
8	STAT3	chr10:45461427-45462285	GM12878	blood:	n/a	chr10:45461703-45461711
9	RELA	chr10:45461250-45462316	GM19193	blood:	n/a	n/a
10	POLR2A	chr10:45458760-45462324	GM12891	blood:	n/a	n/a
11	POLR2A	chr10:45460916-45462344	GM12878	blood:	n/a	n/a
12	YY1	chr10:45461959-45462514	GM12878	blood:	n/a	n/a
13	POLR2A	chr10:45460845-45462395	GM12878	blood:	n/a	n/a
14	CTCF	chr10:45462181-45462581	GM12878	blood:	n/a	chr10:45462392-45462399
15	PAX5	chr10:45461091-45462325	GM12878	blood:	n/a	n/a
16	RELA	chr10:45460706-45462798	GM12891	blood:	n/a	n/a
17	WRNIP1	chr10:45458658-45462963	GM12878	blood:	n/a	n/a
18	CTCF	chr10:45462160-45462310	HBMEC	blood vessel:	n/a	n/a
19	CTCF	chr10:45462160-45462310	HRE	kidney:	n/a	n/a
20	POLR2A	chr10:45458224-45466240	HepG2	liver:	n/a	n/a
21	TBL1XR1	chr10:45461237-45462301	GM12878	blood:	n/a	n/a
22	YY1	chr10:45462166-45462449	GM12892	blood:	n/a	n/a
23	MTA3	chr10:45460328-45462338	GM12878	blood:	n/a	n/a
24	POLR2A	chr10:45460941-45462455	GM12878	blood:	n/a	n/a
25	CTCF	chr10:45462200-45462350	HCM	heart:	n/a	n/a
26	RELA	chr10:45461006-45462288	GM18951	blood:	n/a	n/a
27	RELA	chr10:45461193-45462301	GM19099	blood:	n/a	n/a
28	NFIC	chr10:45461160-45462426	GM12878	blood:	n/a	n/a
29	RELA	chr10:45461229-45462516	GM12878	blood:	n/a	n/a
30	YY1	chr10:45462002-45462392	GM12891	blood:	n/a	n/a
31	ELK1	chr10:45461516-45462245	GM12878	blood:	n/a	chr10:45461777-45461786 chr10:45461777-45461786
32	TBP	chr10:45461182-45462357	GM12878	blood:	n/a	n/a
33	MYC	chr10:45462156-45462881	NB4	blood:	n/a	n/a
34	MXI1	chr10:45461363-45462290	HepG2	liver:	n/a	n/a
35	CTCF	chr10:45462100-45462250	HVMF	connective:	n/a	n/a
36	EBF1	chr10:45461059-45462433	GM12878	blood:	n/a	chr10:45461173-45461182 chr10:45461172-45461182
37	YY1	chr10:45461965-45462350	GM12878	blood:	n/a	n/a
38	CTCF	chr10:45462180-45462330	HAc	cerebellar:	n/a	n/a
39	MAX	chr10:45462127-45462281	NB4	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:45440452..45443413-chr10:45461070..45463781,2	MCF-7	breast:
2	chr10:45462117..45462630-chr10:45470165..45470952,2	MCF-7	breast:
3	chr10:45462150..45464959-chr10:45472680..45475248,4	MCF-7	breast:
4	chr10:45459948..45462747-chr10:45463776..45467477,3	MCF-7	breast:
5	chr10:45460257..45463291-chr10:45472761..45475493,4	MCF-7	breast:
6	chr10:45461482..45464427-chr10:45495628..45497764,2	K562	blood:

No data

Variant related genes	Relation type
RASSF4	TF binding region
ENSG00000107551	Chromatin interaction
ENSG00000165511	Chromatin interaction
ENSG00000165512	Chromatin interaction
ENSG00000165507	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10793572	0.92[ASN][1000 genomes]
rs10793573	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12263146	0.81[CHD][hapmap];0.81[ASN][1000 genomes]
rs3740098	0.83[CEU][hapmap]
rs3814566	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3829908	0.86[CEU][hapmap];0.86[GIH][hapmap];0.94[EUR][1000 genomes]
rs4948938	0.81[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59626742	0.81[ASN][1000 genomes]
rs7914175	0.92[ASN][1000 genomes]
rs883734	0.85[CEU][hapmap]
rs883735	0.83[CEU][hapmap]
rs884879	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs914700	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831846	chr10:45322236-45556370	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1035235	chr10:45442303-45467948	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv526734	chr10:45458485-45492054	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1888983	ZNF32	cis	parietal	SCAN
rs1888983	GDF2	cis	cerebellum	SCAN
rs1888983	RASSF4	cis	multi-tissue	Pritchard

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45455400-45462800	Flanking Active TSS	GM12878-XiMat	blood
2	chr10:45455600-45462600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr10:45455600-45465200	Enhancers	Fetal Thymus	thymus
4	chr10:45455600-45465200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr10:45455800-45463200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr10:45455800-45464000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr10:45455800-45465600	Weak transcription	Ovary	ovary
8	chr10:45456000-45463000	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr10:45456000-45463400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr10:45456200-45463200	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr10:45456200-45463600	Weak transcription	Esophagus	oesophagus
12	chr10:45456200-45465000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr10:45456400-45466200	Weak transcription	Aorta	Aorta
14	chr10:45456600-45462800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr10:45456800-45465200	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr10:45456800-45466600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr10:45458000-45462800	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr10:45458000-45465000	Enhancers	Primary B cells from cord blood	blood
19	chr10:45458200-45462600	Enhancers	Adipose Nuclei	Adipose
20	chr10:45458200-45465000	Enhancers	Thymus	Thymus
21	chr10:45458400-45463000	Enhancers	Fetal Intestine Large	intestine
22	chr10:45458400-45464200	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr10:45458400-45464400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr10:45458400-45464800	Enhancers	Primary B cells from peripheral blood	blood
25	chr10:45458400-45465800	Enhancers	Psoas Muscle	Psoas
26	chr10:45458800-45463800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr10:45458800-45465200	Enhancers	Spleen	Spleen
28	chr10:45459000-45464400	Enhancers	Placenta	Placenta
29	chr10:45459000-45465600	Enhancers	Left Ventricle	heart
30	chr10:45459200-45462800	Weak transcription	Dnd41	blood
31	chr10:45459200-45463000	Enhancers	Fetal Intestine Small	intestine
32	chr10:45459800-45462600	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr10:45459800-45463800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr10:45459800-45465200	Enhancers	Right Ventricle	heart
35	chr10:45459800-45465800	Enhancers	Right Atrium	heart
36	chr10:45460000-45464000	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr10:45460000-45464000	Enhancers	Fetal Kidney	kidney
38	chr10:45460000-45470000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr10:45460200-45463800	Weak transcription	Gastric	stomach
40	chr10:45460400-45462800	Weak transcription	Fetal Stomach	stomach
41	chr10:45460400-45463000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr10:45460400-45463400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr10:45460400-45464000	Enhancers	Fetal Muscle Leg	muscle
44	chr10:45460400-45464400	Weak transcription	Fetal Brain Male	brain
45	chr10:45460400-45464600	Enhancers	Fetal Muscle Trunk	muscle
46	chr10:45460400-45469800	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr10:45460600-45462600	Weak transcription	Liver	Liver
48	chr10:45460600-45462800	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr10:45460600-45463600	Enhancers	Brain Anterior Caudate	brain
50	chr10:45460600-45466200	Weak transcription	Fetal Brain Female	brain

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