Variant report

Variant	rs10838436
Chromosome Location	chr11:45274894-45274895
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:45274069..45275005-chr11:45314850..45315563,4	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1000665	1.00[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.91[MKK][hapmap];0.96[ASN][1000 genomes]
rs11038366	0.90[CHB][hapmap];0.81[CHD][hapmap]
rs11038371	0.96[ASN][1000 genomes]
rs11601021	0.90[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs12278234	0.90[CHB][hapmap]
rs12362429	1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.98[ASN][1000 genomes]
rs12362444	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.93[MKK][hapmap];0.98[ASN][1000 genomes]
rs12362448	0.98[ASN][1000 genomes]
rs2863179	0.96[ASN][1000 genomes]
rs3180446	0.90[CHB][hapmap]
rs4755308	0.94[ASN][1000 genomes]
rs4755940	1.00[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7124508	0.83[GIH][hapmap]
rs751197	0.96[ASN][1000 genomes]
rs751198	1.00[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10838436	SYT13	cis	cerebellum	SCAN
rs10838436	SLC35C1	cis	cerebellum	SCAN
rs10838436	SYT13	cis	Skin Sun Exposed Lower leg	GTEx
rs10838436	PTPMT1	cis	cerebellum	SCAN
rs10838436	ZNF408	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45259800-45279800	Weak transcription	Fetal Brain Male	brain
2	chr11:45264400-45280400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr11:45265400-45281200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr11:45265600-45276400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr11:45267800-45280400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr11:45268200-45275200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr11:45272400-45275600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr11:45272800-45275400	Weak transcription	Fetal Stomach	stomach
9	chr11:45272800-45281200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr11:45273200-45277600	Strong transcription	Fetal Intestine Large	intestine
11	chr11:45273200-45277800	Strong transcription	Fetal Brain Female	brain
12	chr11:45274000-45280600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr11:45274200-45275000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr11:45274400-45280000	Strong transcription	Fetal Intestine Small	intestine
15	chr11:45274400-45280000	Weak transcription	A549	lung
16	chr11:45274400-45281000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr11:45274400-45281200	Weak transcription	Pancreas	Pancrea
18	chr11:45274400-45281400	Weak transcription	Gastric	stomach
19	chr11:45274600-45275400	Weak transcription	HSMMtube	muscle
20	chr11:45274600-45275600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr11:45274600-45277000	Weak transcription	Spleen	Spleen
22	chr11:45274600-45280600	Weak transcription	Colonic Mucosa	Colon
23	chr11:45274600-45281000	Weak transcription	HSMM	muscle
24	chr11:45274800-45275200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr11:45274800-45275200	Weak transcription	NH-A	brain

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