Variant report

Variant	rs12713288
Chromosome Location	chr2:55366639-55366640
allele	A/G
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55343511..55346556-chr2:55364762..55366710,3	K562	blood:
2	chr2:55282373..55283908-chr2:55365419..55368090,2	K562	blood:
3	chr2:55272140..55279868-chr2:55356344..55371606,28	K562	blood:
4	chr2:55276278..55278501-chr2:55364337..55366872,2	MCF-7	breast:
5	chr2:55348151..55351160-chr2:55366268..55368623,3	K562	blood:
6	chr2:55275938..55279901-chr2:55364740..55369438,15	K562	blood:
7	chr2:55366338..55369324-chr2:55384110..55386041,3	K562	blood:
8	chr2:55366570..55369324-chr2:55383738..55386041,2	K562	blood:
9	chr2:55356536..55358953-chr2:55366284..55369182,2	K562	blood:
10	chr2:55366215..55370313-chr2:55376970..55382641,6	K562	blood:
11	chr2:55366215..55370139-chr2:55381125..55383848,4	K562	blood:
12	chr2:55275283..55277414-chr2:55365767..55368496,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10194457	0.82[ASN][1000 genomes]
rs2920842	0.91[GIH][hapmap]
rs4233958	0.84[CHB][hapmap];0.82[ASN][1000 genomes]
rs4672022	0.82[ASN][1000 genomes]
rs6725139	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6731596	0.82[ASN][1000 genomes]
rs6745066	0.83[ASN][1000 genomes]
rs7575639	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs7585618	0.85[CHB][hapmap];0.82[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12713288	EFEMP1	cis	parietal	SCAN
rs12713288	FLJ31438	cis	multi-tissue	Pritchard
rs12713288	NRXN1	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55361400-55370200	Enhancers	Fetal Intestine Large	intestine
2	chr2:55361600-55368200	Weak transcription	Esophagus	oesophagus
3	chr2:55361800-55366800	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr2:55361800-55366800	Weak transcription	Hela-S3	cervix
5	chr2:55361800-55367800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:55361800-55368000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr2:55361800-55368600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:55361800-55368800	Weak transcription	A549	lung
9	chr2:55361800-55373000	Weak transcription	HSMMtube	muscle
10	chr2:55361800-55378600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:55362200-55367600	Weak transcription	Dnd41	blood
12	chr2:55362200-55369000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:55362400-55368800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr2:55363200-55366800	Flanking Active TSS	Brain Hippocampus Middle	brain
15	chr2:55363200-55367200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:55363200-55367800	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr2:55363600-55367200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:55363600-55368800	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr2:55363800-55366800	Enhancers	Rectal Mucosa Donor 29	rectum
20	chr2:55363800-55367200	Enhancers	Stomach Mucosa	stomach
21	chr2:55363800-55368600	Weak transcription	Pancreas	Pancrea
22	chr2:55363800-55370400	Enhancers	Duodenum Mucosa	Duodenum
23	chr2:55364000-55368600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr2:55364200-55369000	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr2:55364800-55367200	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr2:55364800-55367600	Weak transcription	Fetal Thymus	thymus
27	chr2:55364800-55369000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr2:55365000-55367000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr2:55365200-55367000	Weak transcription	Gastric	stomach
30	chr2:55365200-55369000	Flanking Active TSS	K562	blood
31	chr2:55365200-55369200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:55365200-55381000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr2:55365400-55366800	Flanking Active TSS	Brain Anterior Caudate	brain
34	chr2:55365400-55367600	Weak transcription	Fetal Intestine Small	intestine
35	chr2:55365600-55368200	Weak transcription	Right Atrium	heart
36	chr2:55365600-55378600	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr2:55365800-55366800	Active TSS	Rectal Smooth Muscle	rectum
38	chr2:55365800-55367200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr2:55365800-55367200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr2:55365800-55367600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr2:55365800-55369000	Enhancers	Brain Angular Gyrus	brain
42	chr2:55365800-55369000	Enhancers	Brain Cingulate Gyrus	brain
43	chr2:55366000-55367000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr2:55366000-55367000	Weak transcription	Primary hematopoietic stem cells	blood
45	chr2:55366000-55368400	Weak transcription	Small Intestine	intestine
46	chr2:55366000-55368600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr2:55366000-55368600	Weak transcription	Stomach Smooth Muscle	stomach
48	chr2:55366200-55366800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr2:55366200-55368600	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr2:55366200-55368800	Weak transcription	Fetal Stomach	stomach

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