Variant report

Variant	rs2661828
Chromosome Location	chr14:77647602-77647603
allele	C/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	CREB1	chr14:77647522-77648391	H1-hESC	embryonic stem cell:	n/a	n/a
2	YY1	chr14:77647488-77648337	H1-hESC	embryonic stem cell:	n/a	chr14:77648212-77648223 chr14:77648322-77648331
3	TAF1	chr14:77647600-77648416	H1-hESC	embryonic stem cell:	n/a	n/a
4	ELF1	chr14:77647438-77647837	GM12878	blood:	n/a	chr14:77647562-77647573 chr14:77647562-77647573
5	ZNF143	chr14:77647596-77648247	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAX	chr14:77647467-77648874	MCF-7	breast:	n/a	chr14:77648320-77648330 chr14:77648235-77648251
7	GATA1	chr14:77646993-77648051	PBDE	blood:	n/a	n/a
8	REST	chr14:77647551-77649024	H1-neurons	neurons:	n/a	chr14:77648214-77648228 chr14:77648156-77648169 chr14:77648208-77648228 chr14:77647817-77647825 chr14:77648208-77648228 chr14:77648216-77648226
9	MXI1	chr14:77647065-77649126	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr14:77647306-77648876	Raji	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:77640676..77643134-chr14:77646615..77650592,3	MCF-7	breast:
2	chr14:77646733..77650700-chr14:77767687..77771144,4	MCF-7	breast:
3	chr14:77647339..77650955-chr14:77785389..77788358,5	MCF-7	breast:
4	chr14:77646354..77648830-chr14:77666464..77668226,2	MCF-7	breast:
5	chr14:77646577..77649681-chr14:77786771..77790034,4	MCF-7	breast:
6	chr14:77642180..77644687-chr14:77647056..77649855,2	MCF-7	breast:
7	chr14:77646079..77647711-chr14:77656807..77658749,2	MCF-7	breast:
8	chr14:77639432..77641882-chr14:77645275..77647716,2	MCF-7	breast:

Variant related genes	Relation type
TMEM63C	TF binding region
ENSG00000201384	Chromatin interaction
ENSG00000009830	Chromatin interaction
ENSG00000258552	Chromatin interaction
ENSG00000100577	Chromatin interaction
ENSG00000165548	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10147322	0.85[EUR][1000 genomes]
rs1078692	0.80[CEU][hapmap];0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs11159251	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs12881255	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs12883963	0.96[CEU][hapmap];0.88[JPT][hapmap];0.88[EUR][1000 genomes]
rs12891631	0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12896627	0.88[ASN][1000 genomes]
rs1467011	0.91[CHB][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs1504521	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17105457	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1848402	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1861420	0.88[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs207802	0.87[ASN][1000 genomes]
rs207804	0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs2080384	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs2098381	0.88[EUR][1000 genomes]
rs2655996	0.91[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs2655997	0.95[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs28437641	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28713541	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4021320	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs4021325	0.87[ASN][1000 genomes]
rs4899641	0.96[CEU][hapmap];0.88[JPT][hapmap];0.88[EUR][1000 genomes]
rs4903552	0.88[EUR][1000 genomes]
rs61990331	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6574354	0.88[EUR][1000 genomes]
rs6574355	0.88[EUR][1000 genomes]
rs70165	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs7140198	0.80[ASN][1000 genomes]
rs7148276	0.88[EUR][1000 genomes]
rs7148579	0.83[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7154702	0.88[CEU][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8010190	0.88[EUR][1000 genomes]
rs8012358	0.88[EUR][1000 genomes]
rs8012863	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8014837	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs8016243	0.95[CEU][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs8018250	0.95[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs888064	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs9788430	0.87[EUR][1000 genomes]

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	nsv431017	chr14:76938089-77854647	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
2	nsv832834	chr14:77554987-77724357	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv976845	chr14:77621865-77649191	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2661828	TMEM63C	cis	Whole Blood	GTEx

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:77645600-77648000	Weak transcription	Right Atrium	heart
2	chr14:77647000-77648000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr14:77647000-77648000	Enhancers	Esophagus	oesophagus
4	chr14:77647200-77647800	Bivalent Enhancer	HepG2	liver
5	chr14:77647200-77648200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr14:77647400-77647800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
7	chr14:77647400-77647800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr14:77647400-77647800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr14:77647400-77647800	Enhancers	Primary B cells from peripheral blood	blood
10	chr14:77647400-77647800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
11	chr14:77647400-77647800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
12	chr14:77647400-77647800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr14:77647400-77647800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr14:77647400-77647800	Enhancers	Fetal Brain Male	brain
15	chr14:77647400-77648000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr14:77647400-77648000	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr14:77647400-77648000	Bivalent Enhancer	Fetal Intestine Small	intestine
18	chr14:77647400-77648000	Enhancers	Fetal Thymus	thymus
19	chr14:77647400-77648000	Enhancers	K562	blood
20	chr14:77647600-77647800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
21	chr14:77647600-77647800	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr14:77647600-77647800	Flanking Active TSS	H9 Cell Line	embryonic stem cell
23	chr14:77647600-77647800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr14:77647600-77647800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr14:77647600-77647800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr14:77647600-77647800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr14:77647600-77647800	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr14:77647600-77647800	Enhancers	Primary B cells from cord blood	blood
29	chr14:77647600-77647800	Enhancers	Primary hematopoietic stem cells	blood
30	chr14:77647600-77647800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
31	chr14:77647600-77647800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
32	chr14:77647600-77647800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr14:77647600-77647800	Active TSS	Primary T killer memory cells from peripheral blood	blood
34	chr14:77647600-77647800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
35	chr14:77647600-77647800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr14:77647600-77647800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr14:77647600-77647800	Flanking Active TSS	Brain Angular Gyrus	brain
38	chr14:77647600-77647800	Active TSS	Brain Cingulate Gyrus	brain
39	chr14:77647600-77647800	Active TSS	Brain Germinal Matrix	brain
40	chr14:77647600-77647800	Bivalent Enhancer	Brain Hippocampus Middle	brain
41	chr14:77647600-77647800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr14:77647600-77647800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
43	chr14:77647600-77647800	Bivalent Enhancer	Fetal Intestine Large	intestine
44	chr14:77647600-77647800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
45	chr14:77647600-77647800	Enhancers	Pancreas	Pancrea
46	chr14:77647600-77647800	Bivalent/Poised TSS	Right Ventricle	heart
47	chr14:77647600-77647800	Flanking Active TSS	A549	lung
48	chr14:77647600-77647800	Bivalent Enhancer	GM12878-XiMat	blood
49	chr14:77647600-77647800	Enhancers	HMEC	breast
50	chr14:77647600-77647800	Bivalent Enhancer	NH-A	brain

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