Variant report

Variant	rs7257601
Chromosome Location	chr19:42082478-42082479
allele	C/T
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	chr19:42082380-42082684	GM12891	blood:	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	PML	chr19:42082419-42082602	GM12878	blood:	n/a	n/a
8	ZNF263	chr19:42082408-42082845	K562	blood:	n/a	chr19:42082718-42082727
9	POLR2A	chr19:42082396-42082496	HUVEC	blood vessel:	n/a	n/a
10	SPI1	chr19:42082058-42082829	GM12878	blood:	n/a	chr19:42082504-42082511 chr19:42082520-42082527 chr19:42082480-42082493 chr19:42082481-42082494 chr19:42082483-42082492
11	SPI1	chr19:42082235-42082752	HL-60	blood:	n/a	chr19:42082520-42082527 chr19:42082481-42082494 chr19:42082504-42082511 chr19:42082480-42082493 chr19:42082483-42082492
12	POLR2A	chr19:42082444-42082638	MCF-7	breast:	n/a	n/a
13	POLR2A	chr19:42082215-42082757	GM12892	blood:	n/a	n/a
14	SPI1	chr19:42082335-42082644	GM12878	blood:	n/a	chr19:42082520-42082527 chr19:42082481-42082494 chr19:42082504-42082511 chr19:42082480-42082493 chr19:42082483-42082492
15	PAX5	chr19:42082230-42082620	GM12878	blood:	n/a	n/a
16	SRF	chr19:42082056-42082722	MCF-7	breast:	n/a	chr19:42082375-42082392
17	POLR2A	chr19:42082350-42082753	GM18505	blood:	n/a	n/a
18	SRF	chr19:42082096-42082696	HCT-116	colon:	n/a	chr19:42082375-42082392
19	POLR2A	chr19:42082377-42082637	GM12891	blood:	n/a	n/a
20	ZNF263	chr19:42082309-42082899	HEK293-T-REx	kidney:	n/a	chr19:42082718-42082727
21	POLR2A	chr19:42082380-42082737	GM12892	blood:	n/a	n/a
22	SRF	chr19:42082210-42082560	GM12878	blood:	n/a	chr19:42082375-42082392
23	MAZ	chr19:42082414-42082549	K562	blood:	n/a	n/a
24	MTA3	chr19:42082287-42082876	GM12878	blood:	n/a	n/a
25	CTCF	chr19:42082361-42082630	Spleen_OC	spleen:	n/a	n/a
26	POLR2A	chr19:42082355-42082738	GM12878	blood:	n/a	n/a
27	ELK1	chr19:42082191-42082664	GM12878	blood:	n/a	n/a
28	STAT5A	chr19:42082116-42082845	GM12878	blood:	n/a	chr19:42082709-42082721
29	MAZ	chr19:42082309-42082667	GM12878	blood:	n/a	n/a
30	GABPA	chr19:42082232-42082730	HL-60	blood:	n/a	n/a
31	POLR2A	chr19:42082225-42082833	GM12878	blood:	n/a	n/a
32	REST	chr19:42082389-42082566	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr19:42082383-42082748	GM18951	blood:	n/a	n/a
34	POLR2A	chr19:42082316-42082792	GM12892	blood:	n/a	n/a
35	POLR2A	chr19:42082363-42082751	GM12878	blood:	n/a	n/a
36	POLR2A	chr19:42082447-42082644	MCF-7	breast:	n/a	n/a
37	POLR2A	chr19:42082273-42082867	SK-N-MC	brain:	n/a	n/a
38	POLR2A	chr19:42082373-42082747	GM12878	blood:	n/a	n/a
39	SPI1	chr19:42082141-42082830	HL-60	blood:	n/a	chr19:42082520-42082527 chr19:42082481-42082494 chr19:42082504-42082511 chr19:42082480-42082493 chr19:42082483-42082492
40	POLR2A	chr19:42082302-42082757	GM12892	blood:	n/a	n/a
41	SPI1	chr19:42082324-42082626	K562	blood:	n/a	chr19:42082520-42082527 chr19:42082481-42082494 chr19:42082504-42082511 chr19:42082480-42082493 chr19:42082483-42082492
42	SRF	chr19:42082196-42082670	ECC-1	luminal epithelium:	n/a	chr19:42082375-42082392
43	SPI1	chr19:42082311-42082715	GM12878	blood:	n/a	chr19:42082520-42082527 chr19:42082481-42082494 chr19:42082504-42082511 chr19:42082480-42082493 chr19:42082483-42082492
44	SRF	chr19:42082168-42082772	HCT-116	colon:	n/a	chr19:42082375-42082392
45	REST	chr19:42082280-42082826	HL-60	blood:	n/a	n/a
46	SRF	chr19:42082191-42082667	GM12878	blood:	n/a	chr19:42082375-42082392
47	POLR2A	chr19:42082402-42082646	MCF-7	breast:	n/a	n/a
48	POLR2A	chr19:42082344-42082743	GM12891	blood:	n/a	n/a
49	ELF1	chr19:42082220-42082829	GM12878	blood:	n/a	chr19:42082482-42082493
50	SRF	chr19:42082235-42082605	GM12878	blood:	n/a	chr19:42082375-42082392

Variant related genes	Relation type
CEACAM21	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10414811	1.00[CEU][hapmap]
rs10415465	0.83[AFR][1000 genomes]
rs10415860	0.83[AFR][1000 genomes]
rs10418236	1.00[CEU][hapmap]
rs11083638	1.00[CEU][hapmap]
rs11878734	1.00[CEU][hapmap]
rs2231944	1.00[CEU][hapmap]
rs60646575	0.90[AFR][1000 genomes]
rs7257657	0.95[LWK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs8109838	1.00[CEU][hapmap]
rs9653098	1.00[CEU][hapmap]
rs9989667	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv978752	chr19:42082354-42093112	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 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	chr19:42081800-42082600	Enhancers	Primary B cells from peripheral blood	blood
3	chr19:42081800-42082600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr19:42081800-42082600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
5	chr19:42081800-42082800	Enhancers	Left Ventricle	heart
6	chr19:42081800-42083200	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr19:42082000-42082600	Enhancers	Primary hematopoietic stem cells	blood
8	chr19:42082000-42082600	Enhancers	Esophagus	oesophagus
9	chr19:42082000-42082600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
10	chr19:42082000-42082800	Enhancers	Lung	lung
11	chr19:42082000-42082800	Enhancers	Right Ventricle	heart
12	chr19:42082000-42083200	Enhancers	Thymus	Thymus
13	chr19:42082000-42083800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr19:42082000-42084000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr19:42082200-42082600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr19:42082200-42082600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr19:42082200-42082600	Enhancers	Fetal Muscle Leg	muscle
18	chr19:42082200-42082600	Flanking Active TSS	Spleen	Spleen
19	chr19:42082200-42082800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
20	chr19:42082200-42082800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr19:42082200-42082800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
22	chr19:42082200-42082800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr19:42082200-42082800	Enhancers	Right Atrium	heart
24	chr19:42082200-42082800	Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr19:42082200-42083000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
26	chr19:42082200-42083000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr19:42082200-42083000	Flanking Active TSS	GM12878-XiMat	blood
28	chr19:42082200-42085200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr19:42082400-42082600	Bivalent Enhancer	Adipose Nuclei	Adipose
30	chr19:42082400-42082600	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
31	chr19:42082400-42082600	Bivalent Enhancer	HUVEC	blood vessel
32	chr19:42082400-42082800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
33	chr19:42082400-42082800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
34	chr19:42082400-42082800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr19:42082400-42082800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr19:42082400-42082800	Enhancers	Duodenum Mucosa	Duodenum
37	chr19:42082400-42082800	Flanking Active TSS	Fetal Thymus	thymus
38	chr19:42082400-42083000	Flanking Active TSS	Primary T cells from cord blood	blood
39	chr19:42082400-42083000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
40	chr19:42082400-42083200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
41	chr19:42082400-42083200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr19:42082400-42083200	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr19:42082400-42083600	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr19:42082400-42084000	Enhancers	Placenta	Placenta

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