Variant report

Variant	rs12992634
Chromosome Location	chr2:55369761-55369762
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55272140..55279868-chr2:55356344..55371606,28	K562	blood:
2	chr2:55366681..55370422-chr2:55372358..55376649,9	K562	blood:
3	chr2:55366215..55370313-chr2:55376970..55382641,6	K562	blood:
4	chr2:55366215..55370139-chr2:55381125..55383848,4	K562	blood:
5	chr2:55368832..55370528-chr2:55373910..55375514,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10168457	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs10496039	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12988226	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13006159	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13023960	0.83[AMR][1000 genomes]
rs35885020	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59778045	0.80[AMR][1000 genomes]
rs62138263	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6729033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12992634	RTN4	cis	multi-tissue	Pritchard

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55361400-55370200	Enhancers	Fetal Intestine Large	intestine
2	chr2:55361800-55373000	Weak transcription	HSMMtube	muscle
3	chr2:55361800-55378600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr2:55363800-55370400	Enhancers	Duodenum Mucosa	Duodenum
5	chr2:55365200-55381000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:55365600-55378600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr2:55366200-55378600	Weak transcription	Colon Smooth Muscle	Colon
8	chr2:55366800-55373400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:55367200-55370000	Enhancers	Brain Substantia Nigra	brain
10	chr2:55367200-55378800	Weak transcription	Placenta	Placenta
11	chr2:55367600-55369800	Enhancers	Fetal Intestine Small	intestine
12	chr2:55367600-55370000	Enhancers	Stomach Mucosa	stomach
13	chr2:55367800-55375000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:55368400-55369800	Enhancers	Small Intestine	intestine
15	chr2:55368400-55370000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:55368400-55370000	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr2:55368600-55369800	Enhancers	Stomach Smooth Muscle	stomach
18	chr2:55368600-55369800	Bivalent Enhancer	HepG2	liver
19	chr2:55368600-55370000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr2:55368600-55370000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr2:55368600-55370000	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr2:55368800-55369800	Enhancers	Fetal Stomach	stomach
23	chr2:55368800-55369800	Enhancers	A549	lung
24	chr2:55368800-55370200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr2:55368800-55370200	Weak transcription	Brain Hippocampus Middle	brain
26	chr2:55369000-55369800	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr2:55369000-55370600	Enhancers	K562	blood
28	chr2:55369200-55369800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:55369200-55369800	Enhancers	Fetal Lung	lung
30	chr2:55369600-55370200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr2:55369600-55374600	Weak transcription	Hela-S3	cervix

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