Variant report

Variant	rs9749229
Chromosome Location	chr19:42070310-42070311
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:32)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:32 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:42070267-42070605	H1-neurons	neurons:	n/a	n/a
2	RAD21	chr19:42069508-42070332	HCT-116	colon:	n/a	n/a
3	POLR2A	chr19:42069724-42070479	GM12891	blood:	n/a	n/a
4	CTCF	chr19:42069462-42070370	SK-N-SH	brain:	n/a	chr19:42069947-42069956
5	PML	chr19:42069569-42070319	GM12878	blood:	n/a	chr19:42069895-42069903
6	POLR2A	chr19:42069565-42070495	GM15510	blood:	n/a	n/a
7	RAD21	chr19:42069532-42070327	SK-N-SH	brain:	n/a	n/a
8	SP1	chr19:42069609-42070312	A549	lung:	n/a	n/a
9	CTCF	chr19:42069260-42071562	A549	lung:	n/a	chr19:42069947-42069956
10	ELF1	chr19:42069600-42070426	GM12878	blood:	n/a	n/a
11	NFIC	chr19:42070230-42070713	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr19:42069429-42071509	GM12892	blood:	n/a	n/a
13	POLR2A	chr19:42069606-42070598	GM12892	blood:	n/a	n/a
14	POLR2A	chr19:42069481-42070692	GM12892	blood:	n/a	n/a
15	POLR2A	chr19:42069539-42071537	GM12878	blood:	n/a	n/a
16	POLR2A	chr19:42069483-42071341	GM12891	blood:	n/a	n/a
17	RAD21	chr19:42069504-42070352	A549	lung:	n/a	n/a
18	POLR2A	chr19:42069570-42070432	GM18505	blood:	n/a	n/a
19	CTCF	chr19:42070260-42070410	GM12864	blood:	n/a	n/a
20	CTCF	chr19:42070240-42070390	AG09319	gingival:	n/a	n/a
21	CTCF	chr19:42070300-42070450	NHEK	skin:	n/a	n/a
22	RFX5	chr19:42069614-42070506	HepG2	liver:	n/a	n/a
23	POLR2A	chr19:42069596-42070465	GM12878	blood:	n/a	n/a
24	SP1	chr19:42069509-42070424	A549	lung:	n/a	n/a
25	STAT5A	chr19:42069610-42070526	GM12878	blood:	n/a	n/a
26	POLR2A	chr19:42069571-42071073	GM12891	blood:	n/a	n/a
27	BCL3	chr19:42069451-42070328	A549	lung:	n/a	n/a
28	CTCF	chr19:42070260-42070410	K562	blood:	n/a	n/a
29	FOXM1	chr19:42069659-42070401	GM12878	blood:	n/a	n/a
30	MTA3	chr19:42069663-42071390	GM12878	blood:	n/a	n/a
31	POLR2A	chr19:42069385-42070707	GM12892	blood:	n/a	n/a
32	POLR2A	chr19:42069527-42070482	GM12878	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41954861..41955874-chr19:42069542..42070514,6	MCF-7	breast:
2	chr19:41954921..41955448-chr19:42069995..42070621,2	MCF-7	breast:
3	chr19:42048044..42048836-chr19:42069540..42070426,2	K562	blood:
4	chr19:42069422..42070951-chr19:42073170..42075974,2	MCF-7	breast:

No data

Variant related genes	Relation type
CEACAM21	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11881771	0.89[EUR][1000 genomes]
rs16975329	1.00[CEU][hapmap]
rs16975336	1.00[CEU][hapmap]
rs16975348	1.00[CEU][hapmap];0.97[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119418	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119419	0.89[EUR][1000 genomes]
rs62119420	0.89[EUR][1000 genomes]
rs62119421	0.89[EUR][1000 genomes]
rs62119449	0.89[EUR][1000 genomes]
rs62119450	0.89[EUR][1000 genomes]
rs7246864	0.89[EUR][1000 genomes]
rs7255763	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7255775	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7260464	1.00[CEU][hapmap];0.97[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9749229	ARMC10	trans	lymphoblastoid	RTeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42069400-42070400	Enhancers	GM12878-XiMat	blood
2	chr19:42069400-42070800	Bivalent Enhancer	Placenta	Placenta
3	chr19:42069400-42071400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr19:42069400-42077600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr19:42069600-42070400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
6	chr19:42069600-42070400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr19:42069600-42070400	Bivalent Enhancer	Brain Germinal Matrix	brain
8	chr19:42069600-42070400	Enhancers	Pancreas	Pancrea
9	chr19:42069600-42070400	Flanking Bivalent TSS/Enh	A549	lung
10	chr19:42069600-42070800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:42069600-42070800	Enhancers	Primary B cells from peripheral blood	blood
12	chr19:42069600-42070800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
13	chr19:42069600-42071000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr19:42069600-42071200	Bivalent Enhancer	Liver	Liver
15	chr19:42069600-42071200	Enhancers	Lung	lung
16	chr19:42069600-42071200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
17	chr19:42069600-42071200	Bivalent Enhancer	HUVEC	blood vessel
18	chr19:42069600-42071400	Bivalent Enhancer	Colonic Mucosa	Colon
19	chr19:42069600-42071400	Bivalent Enhancer	Left Ventricle	heart
20	chr19:42069600-42071600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr19:42069600-42071800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
22	chr19:42069600-42071800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
23	chr19:42069600-42071800	Bivalent Enhancer	Fetal Intestine Large	intestine
24	chr19:42069600-42071800	Enhancers	Spleen	Spleen
25	chr19:42069600-42072600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr19:42069600-42073000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr19:42069800-42070400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
28	chr19:42069800-42070400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
29	chr19:42069800-42070400	Flanking Active TSS	Primary T cells from cord blood	blood
30	chr19:42069800-42070400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
31	chr19:42069800-42070600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr19:42069800-42070800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
33	chr19:42069800-42070800	Bivalent Enhancer	Fetal Muscle Leg	muscle
34	chr19:42069800-42071200	Enhancers	Gastric	stomach
35	chr19:42069800-42071600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr19:42070000-42070400	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr19:42070000-42070400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
38	chr19:42070000-42070400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
39	chr19:42070000-42070400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr19:42070000-42070400	Flanking Active TSS	HepG2	liver
41	chr19:42070000-42070600	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
42	chr19:42070000-42070600	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
43	chr19:42070000-42070800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
44	chr19:42070000-42070800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
45	chr19:42070000-42070800	Enhancers	Right Atrium	heart
46	chr19:42070000-42070800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
47	chr19:42070000-42071400	Flanking Active TSS	Primary B cells from cord blood	blood
48	chr19:42070000-42071400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr19:42070000-42071400	Bivalent Enhancer	Fetal Thymus	thymus
50	chr19:42070000-42071800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood

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