Variant report

Variant	rs11553574
Chromosome Location	chr3:51737965-51737966
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3A	chr3:51737483-51738017	H1-hESC	embryonic stem cell:	n/a	n/a
2	SPI1	chr3:51737877-51738235	HL-60	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:51737930-51737980	ovcar-3	ovarian:	n/a
2	chr3:51737930-51737980	GM12892	blood:	n/a
3	chr3:51737930-51737980	HRE	kidney:	n/a
4	chr3:51737930-51737980	PANC-1	pancreas:	n/a
5	chr3:51737930-51737980	K562	blood:	n/a
6	chr3:51737930-51737980	HCM	heart:	n/a
7	chr3:51737930-51737980	T-47D	breast:	n/a
8	chr3:51737930-51737980	NHBE	bronchial:	n/a
9	chr3:51737930-51737980	RPTEC	kidney:	n/a
10	chr3:51737930-51737980	AoSMC	blood vessel:	n/a
11	chr3:51737930-51737980	BE2_C	brain:	n/a
12	chr3:51737930-51737980	AG04450	lung:	fetal
13	chr3:51737930-51737980	GM06990	blood:	n/a
14	chr3:51737930-51737980	NHDF-neo	bronchial:	n/a
15	chr3:51737930-51737980	GM19239	blood:	n/a
16	chr3:51737930-51737980	AG09309	skin:	n/a
17	chr3:51737930-51737980	IMR90	lung:	fetal
18	chr3:51737930-51737980	AG10803	skin:	n/a
19	chr3:51737930-51737980	H1-hESC	embryonic stem cell:	embryo
20	chr3:51737930-51737980	HepG2	liver:	n/a
21	chr3:51737930-51737980	LNCaP	prostate:	n/a
22	chr3:51737930-51737980	CMK	blood:	n/a
23	chr3:51737930-51737980	NH-A	brain:	n/a
24	chr3:51737930-51737980	PrEC	prostate:	n/a
25	chr3:51737930-51737980	SK-N-MC	brain:	n/a
26	chr3:51737930-51737980	HRCEpiC	kidney:	n/a
27	chr3:51737930-51737980	MCF10A-Er-Src	breast:	n/a
28	chr3:51737930-51737980	BJ	skin:	n/a
29	chr3:51737930-51737980	MCF-7	breast:	n/a
30	chr3:51737930-51737980	Caco-2	colon:	n/a
31	chr3:51737930-51737980	SK-N-SH_RA	brain:	n/a
32	chr3:51737930-51737980	SKMC	muscle:	n/a
33	chr3:51737930-51737980	HMEC	breast:	n/a
34	chr3:51737930-51737980	A549	lung:	n/a
35	chr3:51737930-51737980	AG09319	gingival:	n/a
36	chr3:51737930-51737980	HCPEpiC	choroid plexus:	n/a
37	chr3:51737930-51737980	AG04449	skin:	fetal
38	chr3:51737930-51737980	Hela-S3	cervix:	n/a
39	chr3:51737930-51737980	HUVEC	blood vessel:	n/a
40	chr3:51737930-51737980	HCT-116	colon:	n/a
41	chr3:51737930-51737980	GM12878	blood:	n/a
42	chr3:51737930-51737980	U87	brain:	n/a
43	chr3:51737930-51737980	ECC-1	luminal epithelium:	n/a
44	chr3:51737930-51737980	NT2-D1	testis:	n/a
45	chr3:51737930-51737980	GM12891	blood:	n/a
46	chr3:51737930-51737980	HIPEpiC	eye:	n/a
47	chr3:51737930-51737980	HL-60	blood:	n/a
48	chr3:51737930-51737980	SK-N-SH	brain:	n/a
49	chr3:51737930-51737980	NB4	blood:	n/a
50	chr3:51737930-51737980	HNPCEpiC	eye:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:51464596..51467000-chr3:51736520..51738058,2	MCF-7	breast:
2	chr3:51726622..51728769-chr3:51737176..51738724,2	MCF-7	breast:

No data

Variant related genes	Relation type
GRM2	TF binding region
GRM2	CpG island
ENSG00000201595	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12485825	0.88[ASN][1000 genomes]
rs12487957	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12493092	0.93[EUR][1000 genomes]
rs12496340	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13324384	0.87[EUR][1000 genomes]
rs2132914	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4687592	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4687599	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4687769	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4687773	0.93[EUR][1000 genomes]
rs4687774	0.93[EUR][1000 genomes]
rs55706150	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55872019	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59034236	0.93[EUR][1000 genomes]
rs59955041	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72951490	0.87[EUR][1000 genomes]
rs7375146	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73834265	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	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	esv1814919	chr3:51703488-51752684	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv3410055	chr3:51737012-51741510	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51706400-51741000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:51706600-51739600	Weak transcription	Small Intestine	intestine
3	chr3:51707800-51740400	Strong transcription	Fetal Intestine Small	intestine
4	chr3:51708800-51738800	Strong transcription	Fetal Intestine Large	intestine
5	chr3:51716400-51741200	Weak transcription	Fetal Kidney	kidney
6	chr3:51716800-51738800	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr3:51717400-51739800	Strong transcription	Liver	Liver
8	chr3:51719600-51741200	Weak transcription	NHDF-Ad	bronchial
9	chr3:51720600-51739800	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr3:51720600-51740000	Strong transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:51721000-51738200	Weak transcription	A549	lung
12	chr3:51721000-51741000	Weak transcription	HUVEC	blood vessel
13	chr3:51721400-51738800	Strong transcription	Colonic Mucosa	Colon
14	chr3:51721400-51739400	Strong transcription	Thymus	Thymus
15	chr3:51721400-51739800	Strong transcription	Duodenum Mucosa	Duodenum
16	chr3:51721400-51740000	Strong transcription	Placenta	Placenta
17	chr3:51721400-51740200	Strong transcription	Esophagus	oesophagus
18	chr3:51721400-51740400	Strong transcription	Dnd41	blood
19	chr3:51721400-51740600	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr3:51721400-51740800	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr3:51721600-51739400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:51721600-51740400	Strong transcription	Fetal Stomach	stomach
23	chr3:51721600-51740800	Weak transcription	HSMM	muscle
24	chr3:51721800-51740200	Strong transcription	Stomach Smooth Muscle	stomach
25	chr3:51722200-51739200	Strong transcription	Fetal Muscle Leg	muscle
26	chr3:51722400-51739000	Strong transcription	Fetal Muscle Trunk	muscle
27	chr3:51722400-51740200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr3:51722600-51740000	Strong transcription	Primary B cells from peripheral blood	blood
29	chr3:51722600-51741200	Weak transcription	Stomach Mucosa	stomach
30	chr3:51723200-51738600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:51723800-51738200	Strong transcription	Fetal Thymus	thymus
32	chr3:51723800-51739400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:51724000-51739000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:51724000-51740200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr3:51724000-51740400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:51724400-51741200	Weak transcription	Primary hematopoietic stem cells	blood
37	chr3:51725400-51740800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr3:51725600-51740000	Strong transcription	Lung	lung
39	chr3:51725600-51740200	Strong transcription	Gastric	stomach
40	chr3:51726200-51738800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:51727000-51739200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:51727400-51740200	Weak transcription	Psoas Muscle	Psoas
43	chr3:51728000-51739600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr3:51728200-51738800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr3:51728200-51740200	Strong transcription	Adipose Nuclei	Adipose
46	chr3:51728400-51739400	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr3:51728400-51740000	Strong transcription	Aorta	Aorta
48	chr3:51728800-51740000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:51729000-51739400	Strong transcription	Brain Hippocampus Middle	brain
50	chr3:51729000-51740200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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