Variant report

Variant	rs11879090
Chromosome Location	chr19:41917260-41917261
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:41915352..41917525-chr19:41928842..41931188,2	MCF-7	breast:
2	chr19:41911962..41915322-chr19:41916825..41920523,3	K562	blood:
3	chr19:41899828..41905293-chr19:41906916..41917787,16	MCF-7	breast:
4	chr19:41903791..41906982-chr19:41915611..41919642,3	K562	blood:

Variant related genes	Relation type
ENSG00000268987	Chromatin interaction
ENSG00000077348	Chromatin interaction
ENSG00000248098	Chromatin interaction

Extended variants
information (count: 2 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs284647	0.81[CHB][hapmap];0.94[YRI][hapmap]
rs284653	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11879090	TBC1D17	cis	parietal	SCAN
rs11879090	SIX5	cis	cerebellum	SCAN
rs11879090	ATP5SL	trans	parietal	SCAN
rs11879090	PHLDB3	cis	parietal	SCAN
rs11879090	LYPD5	cis	parietal	SCAN
rs11879090	DEDD2	cis	cerebellum	SCAN
rs11879090	NOSIP	cis	parietal	SCAN
rs11879090	PSG2	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41904600-41924800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:41905000-41924800	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr19:41905000-41930800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr19:41905200-41917400	Weak transcription	Brain Substantia Nigra	brain
5	chr19:41905200-41917600	Weak transcription	HSMMtube	muscle
6	chr19:41905200-41926600	Weak transcription	Small Intestine	intestine
7	chr19:41913600-41925800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr19:41913800-41917800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:41913800-41919400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr19:41913800-41919600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr19:41913800-41921000	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr19:41913800-41927000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr19:41913800-41932600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr19:41914000-41917800	Enhancers	Stomach Mucosa	stomach
15	chr19:41914400-41917800	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr19:41914400-41918200	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr19:41914400-41918200	Enhancers	Fetal Heart	heart
18	chr19:41914600-41918800	Strong transcription	Fetal Muscle Trunk	muscle
19	chr19:41914800-41918200	Enhancers	Right Atrium	heart
20	chr19:41915000-41918200	Enhancers	HMEC	breast
21	chr19:41915200-41918800	Weak transcription	Fetal Brain Male	brain
22	chr19:41915200-41932600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr19:41915400-41918200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr19:41915400-41932800	Weak transcription	Hela-S3	cervix
25	chr19:41915600-41917400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr19:41915600-41932800	Weak transcription	NH-A	brain
27	chr19:41915800-41917600	Weak transcription	NHEK	skin
28	chr19:41915800-41918200	Enhancers	Right Ventricle	heart
29	chr19:41915800-41920200	Weak transcription	A549	lung
30	chr19:41916000-41917400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr19:41916000-41918400	Enhancers	Psoas Muscle	Psoas
32	chr19:41916000-41919000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr19:41916000-41924200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr19:41916000-41932000	Strong transcription	Fetal Stomach	stomach
35	chr19:41916000-41932400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr19:41916200-41917600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr19:41916200-41917800	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr19:41916200-41919000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr19:41916200-41919600	Strong transcription	Fetal Intestine Small	intestine
40	chr19:41916200-41921600	Strong transcription	NHLF	lung
41	chr19:41916200-41922200	Weak transcription	Osteobl	bone
42	chr19:41916200-41926200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr19:41916200-41927000	Strong transcription	Placenta	Placenta
44	chr19:41916200-41928000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr19:41916200-41932000	Weak transcription	HUVEC	blood vessel
46	chr19:41916400-41917400	Strong transcription	Brain Anterior Caudate	brain
47	chr19:41916400-41917400	Strong transcription	Brain Cingulate Gyrus	brain
48	chr19:41916400-41917400	Weak transcription	GM12878-XiMat	blood
49	chr19:41916400-41918000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr19:41916400-41918000	Genic enhancers	Lung	lung

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