Variant report

Variant	rs55844314
Chromosome Location	chr3:46036264-46036265
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:45979978..45982491-chr3:46035904..46038054,2	MCF-7	breast:
2	chr3:45639893..45641594-chr3:46034221..46037019,2	K562	blood:
3	chr3:46035149..46036764-chr3:46100668..46103208,2	K562	blood:
4	chr3:45999931..46002048-chr3:46035446..46037262,2	MCF-7	breast:
5	chr3:46019979..46023374-chr3:46034093..46037294,5	K562	blood:
6	chr3:46036059..46037983-chr3:46447594..46449867,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-XCR1-2	chr3:46033520-46037161	ucscGeneNc_uc003cpd_1

No data

Variant related genes	Relation type
ENSG00000163820	Chromatin interaction
ENSG00000223552	Chromatin interaction
ENSG00000121797	Chromatin interaction
ENSG00000172215	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11130078	0.84[ASN][1000 genomes]
rs12053895	0.88[ASN][1000 genomes]
rs12485445	0.88[ASN][1000 genomes]
rs13064616	0.92[ASN][1000 genomes]
rs13084541	0.82[ASN][1000 genomes]
rs1392288	1.00[ASN][1000 genomes]
rs1463680	0.88[ASN][1000 genomes]
rs1500003	1.00[ASN][1000 genomes]
rs1846615	1.00[ASN][1000 genomes]
rs1873001	1.00[ASN][1000 genomes]
rs2129879	0.92[ASN][1000 genomes]
rs2129881	0.92[ASN][1000 genomes]
rs2133660	1.00[ASN][1000 genomes]
rs2171528	0.92[ASN][1000 genomes]
rs2171529	0.92[ASN][1000 genomes]
rs2234350	0.88[ASN][1000 genomes]
rs2276855	0.96[ASN][1000 genomes]
rs2276856	0.82[ASN][1000 genomes]
rs2373089	0.88[ASN][1000 genomes]
rs2373090	0.88[ASN][1000 genomes]
rs35283688	0.88[ASN][1000 genomes]
rs3796374	1.00[ASN][1000 genomes]
rs3947589	1.00[ASN][1000 genomes]
rs4683165	0.91[ASN][1000 genomes]
rs57542549	0.82[ASN][1000 genomes]
rs57651127	0.96[ASN][1000 genomes]
rs57837898	0.96[ASN][1000 genomes]
rs751667	0.96[ASN][1000 genomes]
rs7612402	0.92[ASN][1000 genomes]
rs9844821	1.00[ASN][1000 genomes]
rs9869848	0.88[ASN][1000 genomes]
rs9875616	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv2756987	chr3:46016464-46120400	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv2759145	chr3:46016464-46120400	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv1805205	chr3:46032847-46111081	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46033800-46036400	Flanking Active TSS	GM12878-XiMat	blood
2	chr3:46034600-46037000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
3	chr3:46034800-46036600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:46035000-46036400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
5	chr3:46035400-46036400	Flanking Active TSS	Fetal Thymus	thymus
6	chr3:46035400-46036400	Flanking Active TSS	Thymus	Thymus
7	chr3:46035400-46036400	Flanking Active TSS	Dnd41	blood
8	chr3:46035600-46036400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr3:46035800-46036400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr3:46035800-46036400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
11	chr3:46035800-46036400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr3:46035800-46036400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:46035800-46036400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:46035800-46036400	Flanking Active TSS	Rectal Smooth Muscle	rectum
15	chr3:46035800-46036400	Flanking Active TSS	Stomach Smooth Muscle	stomach
16	chr3:46035800-46036400	Flanking Active TSS	K562	blood
17	chr3:46035800-46036400	Flanking Active TSS	NHDF-Ad	bronchial
18	chr3:46035800-46036400	Flanking Active TSS	NHLF	lung
19	chr3:46035800-46036600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:46035800-46036800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:46035800-46037000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr3:46035800-46037600	Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr3:46035800-46037800	Active TSS	Right Atrium	heart
24	chr3:46036000-46036400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:46036000-46036400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr3:46036000-46036400	Flanking Active TSS	Primary T cells from cord blood	blood
27	chr3:46036000-46036400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
28	chr3:46036000-46036400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr3:46036000-46036400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:46036000-46036400	Flanking Active TSS	Colon Smooth Muscle	Colon
31	chr3:46036000-46036400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
32	chr3:46036000-46036400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr3:46036000-46036600	Active TSS	Fetal Brain Female	brain
34	chr3:46036000-46037000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:46036000-46037000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr3:46036000-46037400	Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr3:46036000-46037400	Active TSS	NH-A	brain
38	chr3:46036000-46037600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:46036000-46037600	Active TSS	Aorta	Aorta
40	chr3:46036000-46037600	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr3:46036000-46037600	Active TSS	Ovary	ovary
42	chr3:46036000-46037600	Active TSS	Hela-S3	cervix
43	chr3:46036000-46037800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
44	chr3:46036000-46037800	Active TSS	Colonic Mucosa	Colon
45	chr3:46036000-46037800	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr3:46036000-46037800	Active TSS	Right Ventricle	heart
47	chr3:46036000-46038000	Active TSS	Rectal Mucosa Donor 29	rectum
48	chr3:46036200-46036400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
49	chr3:46036200-46036400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr3:46036200-46036400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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