Variant report

Variant	rs7257657
Chromosome Location	chr19:42082326-42082327
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	chr19:42082278-42082370	HUVEC	blood vessel:	n/a	n/a
2	SRF	chr19:42082092-42082554	GM12878	blood:	n/a	chr19:42082375-42082392
3	SPI1	chr19:42082322-42082640	K562	blood:	n/a	chr19:42082520-42082527 chr19:42082481-42082494 chr19:42082504-42082511 chr19:42082480-42082493 chr19:42082483-42082492
4	POLR2A	chr19:42082217-42082819	HL-60	blood:	n/a	n/a
5	SPI1	chr19:42082207-42082720	GM12891	blood:	n/a	chr19:42082520-42082527 chr19:42082481-42082494 chr19:42082504-42082511 chr19:42082480-42082493 chr19:42082483-42082492
6	POLR2A	chr19:42082284-42082756	HL-60	blood:	n/a	n/a
7	SPI1	chr19:42082058-42082829	GM12878	blood:	n/a	chr19:42082504-42082511 chr19:42082520-42082527 chr19:42082480-42082493 chr19:42082481-42082494 chr19:42082483-42082492
8	SPI1	chr19:42082235-42082752	HL-60	blood:	n/a	chr19:42082520-42082527 chr19:42082481-42082494 chr19:42082504-42082511 chr19:42082480-42082493 chr19:42082483-42082492
9	POLR2A	chr19:42082215-42082757	GM12892	blood:	n/a	n/a
10	PAX5	chr19:42082230-42082620	GM12878	blood:	n/a	n/a
11	SRF	chr19:42082056-42082722	MCF-7	breast:	n/a	chr19:42082375-42082392
12	SRF	chr19:42082096-42082696	HCT-116	colon:	n/a	chr19:42082375-42082392
13	ZNF263	chr19:42082309-42082899	HEK293-T-REx	kidney:	n/a	chr19:42082718-42082727
14	SRF	chr19:42082210-42082560	GM12878	blood:	n/a	chr19:42082375-42082392
15	MTA3	chr19:42082287-42082876	GM12878	blood:	n/a	n/a
16	ELK1	chr19:42082191-42082664	GM12878	blood:	n/a	n/a
17	STAT5A	chr19:42082116-42082845	GM12878	blood:	n/a	chr19:42082709-42082721
18	MAZ	chr19:42082309-42082667	GM12878	blood:	n/a	n/a
19	GABPA	chr19:42082232-42082730	HL-60	blood:	n/a	n/a
20	POLR2A	chr19:42082225-42082833	GM12878	blood:	n/a	n/a
21	POLR2A	chr19:42082316-42082792	GM12892	blood:	n/a	n/a
22	POLR2A	chr19:42082273-42082867	SK-N-MC	brain:	n/a	n/a
23	SPI1	chr19:42082141-42082830	HL-60	blood:	n/a	chr19:42082520-42082527 chr19:42082481-42082494 chr19:42082504-42082511 chr19:42082480-42082493 chr19:42082483-42082492
24	POLR2A	chr19:42082302-42082757	GM12892	blood:	n/a	n/a
25	SPI1	chr19:42082324-42082626	K562	blood:	n/a	chr19:42082520-42082527 chr19:42082481-42082494 chr19:42082504-42082511 chr19:42082480-42082493 chr19:42082483-42082492
26	SRF	chr19:42082196-42082670	ECC-1	luminal epithelium:	n/a	chr19:42082375-42082392
27	SPI1	chr19:42082311-42082715	GM12878	blood:	n/a	chr19:42082520-42082527 chr19:42082481-42082494 chr19:42082504-42082511 chr19:42082480-42082493 chr19:42082483-42082492
28	SRF	chr19:42082168-42082772	HCT-116	colon:	n/a	chr19:42082375-42082392
29	REST	chr19:42082280-42082826	HL-60	blood:	n/a	n/a
30	SRF	chr19:42082191-42082667	GM12878	blood:	n/a	chr19:42082375-42082392
31	ELF1	chr19:42082220-42082829	GM12878	blood:	n/a	chr19:42082482-42082493
32	SRF	chr19:42082326-42082459	HepG2	liver:	n/a	chr19:42082375-42082392
33	SRF	chr19:42082235-42082605	GM12878	blood:	n/a	chr19:42082375-42082392
34	ELF1	chr19:42082323-42082648	K562	blood:	n/a	chr19:42082482-42082493
35	SRF	chr19:42082010-42082780	MCF-7	breast:	n/a	chr19:42082375-42082392
36	POLR2A	chr19:42082218-42082731	GM12878	blood:	n/a	n/a
37	SRF	chr19:42082137-42082693	ECC-1	luminal epithelium:	n/a	chr19:42082375-42082392
38	SPI1	chr19:42082272-42082713	GM12891	blood:	n/a	chr19:42082520-42082527 chr19:42082481-42082494 chr19:42082504-42082511 chr19:42082480-42082493 chr19:42082483-42082492

Variant related genes	Relation type
CEACAM21	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10406221	0.87[CHD][hapmap]
rs10409976	0.91[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs10415465	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10415860	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10421584	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10421785	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12709854	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12709855	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17724225	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1860255	0.83[CHB][hapmap]
rs2191019	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs2302188	0.83[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs28433747	0.90[ASN][1000 genomes]
rs28709791	0.96[ASN][1000 genomes]
rs34007391	0.95[ASN][1000 genomes]
rs35834169	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3745938	0.95[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.91[ASN][1000 genomes]
rs57979746	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58163879	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60646575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs714106	0.87[CHD][hapmap]
rs7247842	0.95[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs7251994	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7257601	0.95[LWK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs740591	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs758350	0.95[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.88[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[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	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
4	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
5	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
6	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
7	nsv960930	chr19:42080172-42093112	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7257657	CEACAM21	cis	multi-tissue	Pritchard
rs7257657	CEACAM21	cis	lymphoblastoid	seeQTL
rs7257657	R29124_1	cis	multi-tissue	Pritchard

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42081600-42083000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr19:42081800-42082400	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr19:42081800-42082400	Enhancers	Primary B cells from cord blood	blood
4	chr19:42081800-42082400	Enhancers	Primary T cells from cord blood	blood
5	chr19:42081800-42082400	Enhancers	Primary T cells fromperipheralblood	blood
6	chr19:42081800-42082400	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr19:42081800-42082400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr19:42081800-42082400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr19:42081800-42082400	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr19:42081800-42082400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr19:42081800-42082600	Enhancers	Primary B cells from peripheral blood	blood
12	chr19:42081800-42082600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr19:42081800-42082600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr19:42081800-42082800	Enhancers	Left Ventricle	heart
15	chr19:42081800-42083200	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr19:42082000-42082600	Enhancers	Primary hematopoietic stem cells	blood
17	chr19:42082000-42082600	Enhancers	Esophagus	oesophagus
18	chr19:42082000-42082600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
19	chr19:42082000-42082800	Enhancers	Lung	lung
20	chr19:42082000-42082800	Enhancers	Right Ventricle	heart
21	chr19:42082000-42083200	Enhancers	Thymus	Thymus
22	chr19:42082000-42083800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr19:42082000-42084000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr19:42082200-42082400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
25	chr19:42082200-42082400	Flanking Active TSS	Duodenum Mucosa	Duodenum
26	chr19:42082200-42082400	Enhancers	Fetal Thymus	thymus
27	chr19:42082200-42082400	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
28	chr19:42082200-42082600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr19:42082200-42082600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
30	chr19:42082200-42082600	Enhancers	Fetal Muscle Leg	muscle
31	chr19:42082200-42082600	Flanking Active TSS	Spleen	Spleen
32	chr19:42082200-42082800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr19:42082200-42082800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr19:42082200-42082800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
35	chr19:42082200-42082800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr19:42082200-42082800	Enhancers	Right Atrium	heart
37	chr19:42082200-42082800	Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr19:42082200-42083000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr19:42082200-42083000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr19:42082200-42083000	Flanking Active TSS	GM12878-XiMat	blood
41	chr19:42082200-42085200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

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