Variant report

Variant	rs11083627
Chromosome Location	chr19:42069900-42069901
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	SP1	chr19:42069842-42070258	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr19:42069803-42070073	NHEK	skin:	n/a	chr19:42069947-42069956
3	MAX	chr19:42069757-42070058	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr19:42069648-42070243	MCF-7	breast:	n/a	chr19:42069947-42069956
5	EP300	chr19:42069690-42070031	GM12878	blood:	n/a	n/a
6	CTCF	chr19:42069880-42070030	AG09309	skin:	n/a	chr19:42069947-42069956
7	SMC3	chr19:42069794-42070104	K562	blood:	n/a	n/a
8	MAX	chr19:42069741-42070064	K562	blood:	n/a	n/a
9	MAFF	chr19:42069780-42070118	HepG2	liver:	n/a	n/a
10	MYC	chr19:42069707-42070120	NB4	blood:	n/a	n/a
11	CTCF	chr19:42069823-42070075	HUVEC	blood vessel:	n/a	chr19:42069947-42069956
12	YY1	chr19:42069788-42070294	A549	lung:	n/a	n/a
13	CTCF	chr19:42069880-42070030	K562	blood:	n/a	chr19:42069947-42069956
14	CTCF	chr19:42069800-42070070	GM13977	blood:	n/a	chr19:42069947-42069956
15	RAD21	chr19:42069508-42070332	HCT-116	colon:	n/a	n/a
16	HDAC2	chr19:42069769-42070167	HepG2	liver:	n/a	chr19:42069904-42069923
17	CTCF	chr19:42069812-42070053	SK-N-SH_RA	brain:	n/a	chr19:42069947-42069956
18	POLR2A	chr19:42069724-42070479	GM12891	blood:	n/a	n/a
19	CTCF	chr19:42069860-42070010	BE2_C	brain:	n/a	chr19:42069947-42069956
20	CTCF	chr19:42069747-42070148	K562	blood:	n/a	chr19:42069947-42069956
21	TBL1XR1	chr19:42069755-42070106	GM12878	blood:	n/a	n/a
22	RAD21	chr19:42069594-42070249	A549	lung:	n/a	n/a
23	CTCF	chr19:42069860-42070010	HVMF	connective:	n/a	chr19:42069947-42069956
24	CTCF	chr19:42069462-42070370	SK-N-SH	brain:	n/a	chr19:42069947-42069956
25	MAZ	chr19:42069824-42070072	K562	blood:	n/a	n/a
26	NRF1	chr19:42069674-42070063	H1-hESC	embryonic stem cell:	n/a	chr19:42069867-42069878 chr19:42069864-42069878
27	CTCF	chr19:42069880-42070030	GM12866	blood:	n/a	chr19:42069947-42069956
28	CTCF	chr19:42069860-42070010	AG09309	skin:	n/a	chr19:42069947-42069956
29	POLR2A	chr19:42069751-42069968	GM12878	blood:	n/a	n/a
30	PML	chr19:42069569-42070319	GM12878	blood:	n/a	chr19:42069895-42069903
31	MYBL2	chr19:42069767-42070102	HepG2	liver:	n/a	n/a
32	CTCF	chr19:42069730-42070137	A549	lung:	n/a	chr19:42069947-42069956
33	CTCF	chr19:42069880-42070030	BE2_C	brain:	n/a	chr19:42069947-42069956
34	CTCF	chr19:42069880-42070030	BJ	skin:	n/a	chr19:42069947-42069956
35	POLR2A	chr19:42069565-42070495	GM15510	blood:	n/a	n/a
36	CTCF	chr19:42069840-42069990	GM12869	blood:	n/a	chr19:42069947-42069956
37	CTCF	chr19:42069880-42070030	NHEK	skin:	n/a	chr19:42069947-42069956
38	RAD21	chr19:42069640-42070149	H1-hESC	embryonic stem cell:	n/a	n/a
39	NRF1	chr19:42069726-42070071	HepG2	liver:	n/a	chr19:42069867-42069878 chr19:42069864-42069878
40	CTCF	chr19:42069860-42070010	HUVEC	blood vessel:	n/a	chr19:42069947-42069956
41	CTCF	chr19:42069860-42070010	GM12868	blood:	n/a	chr19:42069947-42069956
42	TCF12	chr19:42069338-42070279	A549	lung:	n/a	n/a
43	CTCF	chr19:42069829-42070067	GM10266	blood:	n/a	chr19:42069947-42069956
44	RAD21	chr19:42069532-42070327	SK-N-SH	brain:	n/a	n/a
45	CTCF	chr19:42069860-42070010	SK-N-SH_RA	brain:	n/a	chr19:42069947-42069956
46	BACH1	chr19:42069740-42070116	H1-hESC	embryonic stem cell:	n/a	n/a
47	SP4	chr19:42069730-42070058	H1-hESC	embryonic stem cell:	n/a	n/a
48	CTCF	chr19:42069880-42070030	HRPEpiC	eye:	n/a	chr19:42069947-42069956
49	SP1	chr19:42069609-42070312	A549	lung:	n/a	n/a
50	CTCF	chr19:42069829-42070060	HepG2	liver:	n/a	chr19:42069947-42069956

No.	Distal block	Cell Line	Cell type
1	chr19:41955026..41955865-chr19:42069595..42070117,2	K562	blood:
2	chr19:41954861..41955874-chr19:42069542..42070514,6	MCF-7	breast:
3	chr19:42048044..42048836-chr19:42069540..42070426,2	K562	blood:
4	chr19:42069422..42070951-chr19:42073170..42075974,2	MCF-7	breast:
5	chr19:41847464..41848006-chr19:42069412..42069986,2	MCF-7	breast:

Variant related genes	Relation type
CEACAM21	TF binding region
ENSG00000105329	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10153482	0.92[ASN][1000 genomes]
rs10405039	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10406221	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10409976	0.87[JPT][hapmap]
rs10420992	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10421574	0.94[ASN][1000 genomes]
rs10421584	0.87[JPT][hapmap]
rs10423808	0.82[ASN][1000 genomes]
rs10424376	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs11083626	0.81[ASN][1000 genomes]
rs11083628	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11083629	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11673075	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12150975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12462194	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12983999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1860255	0.95[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2005606	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2191019	0.95[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2302188	0.85[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2317314	0.95[CHB][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs34054275	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3745936	0.91[CHB][hapmap]
rs3745938	0.86[JPT][hapmap]
rs4802120	0.82[ASN][1000 genomes]
rs4802122	0.81[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs4803479	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803481	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs714106	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7247842	0.82[JPT][hapmap]
rs7255742	0.81[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs7257282	0.80[ASN][1000 genomes]
rs7257565	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs758350	0.82[JPT][hapmap]
rs873910	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[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	nsv911771	chr19:41962486-42085873	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv911773	chr19:42001210-42085873	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv978751	chr19:42036596-42073874	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1057624	chr19:42057334-42152828	Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1058847	chr19:42057334-42172442	Bivalent/Poised TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv1063241	chr19:42057334-42175160	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv519408	chr19:42066279-42171906	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11083627	CEACAMP3	cis	Whole Blood	GTEx
rs11083627	CEACAM21	cis	multi-tissue	Pritchard
rs11083627	CEACAMP3	cis	lung	GTEx
rs11083627	CEACAM21	cis	Lymphoblastoid	GTEx
rs11083627	CEACAM21	Cis_1M	lymphoblastoid	RTeQTL
rs11083627	CEACAM21	cis	lung	GTEx
rs11083627	R29124_1	cis	multi-tissue	Pritchard
rs11083627	CEACAM21	cis	Thyroid	GTEx
rs11083627	AC011526.1	cis	Adipose Subcutaneous	GTEx
rs11083627	CEACAM21	cis	Whole Blood	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42062200-42070000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr19:42067200-42070000	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr19:42069400-42070000	Enhancers	Primary B cells from cord blood	blood
4	chr19:42069400-42070000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr19:42069400-42070400	Enhancers	GM12878-XiMat	blood
6	chr19:42069400-42070800	Bivalent Enhancer	Placenta	Placenta
7	chr19:42069400-42071400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr19:42069400-42077600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr19:42069600-42070000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
10	chr19:42069600-42070000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
11	chr19:42069600-42070000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
12	chr19:42069600-42070000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr19:42069600-42070000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr19:42069600-42070000	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr19:42069600-42070000	Enhancers	Primary hematopoietic stem cells	blood
16	chr19:42069600-42070000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr19:42069600-42070000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr19:42069600-42070000	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr19:42069600-42070000	Enhancers	Fetal Thymus	thymus
20	chr19:42069600-42070000	Active TSS	Right Atrium	heart
21	chr19:42069600-42070000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr19:42069600-42070200	Bivalent Enhancer	Adipose Nuclei	Adipose
23	chr19:42069600-42070200	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
24	chr19:42069600-42070200	Enhancers	Esophagus	oesophagus
25	chr19:42069600-42070400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
26	chr19:42069600-42070400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr19:42069600-42070400	Bivalent Enhancer	Brain Germinal Matrix	brain
28	chr19:42069600-42070400	Enhancers	Pancreas	Pancrea
29	chr19:42069600-42070400	Flanking Bivalent TSS/Enh	A549	lung
30	chr19:42069600-42070800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:42069600-42070800	Enhancers	Primary B cells from peripheral blood	blood
32	chr19:42069600-42070800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
33	chr19:42069600-42071000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr19:42069600-42071200	Bivalent Enhancer	Liver	Liver
35	chr19:42069600-42071200	Enhancers	Lung	lung
36	chr19:42069600-42071200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
37	chr19:42069600-42071200	Bivalent Enhancer	HUVEC	blood vessel
38	chr19:42069600-42071400	Bivalent Enhancer	Colonic Mucosa	Colon
39	chr19:42069600-42071400	Bivalent Enhancer	Left Ventricle	heart
40	chr19:42069600-42071600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr19:42069600-42071800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
42	chr19:42069600-42071800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr19:42069600-42071800	Bivalent Enhancer	Fetal Intestine Large	intestine
44	chr19:42069600-42071800	Enhancers	Spleen	Spleen
45	chr19:42069600-42072600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr19:42069600-42073000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr19:42069800-42070000	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr19:42069800-42070000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr19:42069800-42070000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr19:42069800-42070000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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