Variant report

Variant	rs9504481
Chromosome Location	chr6:5654712-5654713
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10484315	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17141110	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17141115	0.86[EUR][1000 genomes]
rs9504478	1.00[CEU][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916361	chr6:5315853-5695486	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv600887	chr6:5545046-5694713	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9504481	F13A1	cis	lymphoblastoid	seeQTL
rs9504481	NRN1	cis	lymphoblastoid	seeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5641200-5663400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr6:5641200-5664000	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr6:5641400-5656400	Weak transcription	Esophagus	oesophagus
4	chr6:5641400-5658800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr6:5641400-5660800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr6:5641400-5663400	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr6:5641400-5664400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr6:5641400-5665200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr6:5641400-5665400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr6:5641400-5673800	Weak transcription	Fetal Intestine Small	intestine
11	chr6:5641600-5655600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:5641600-5665400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr6:5641600-5671400	Weak transcription	Lung	lung
14	chr6:5642000-5659600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:5642000-5659800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:5642200-5672400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:5644000-5655600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr6:5644200-5655800	Weak transcription	Spleen	Spleen
19	chr6:5645400-5666200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:5645800-5655400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr6:5646000-5655600	Weak transcription	Fetal Muscle Leg	muscle
22	chr6:5646200-5662600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr6:5648200-5664000	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr6:5648200-5664200	Weak transcription	Primary B cells from peripheral blood	blood
25	chr6:5649800-5655600	Weak transcription	Aorta	Aorta
26	chr6:5650000-5671400	Weak transcription	Small Intestine	intestine
27	chr6:5651200-5671400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr6:5651400-5663800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr6:5652600-5655600	Weak transcription	Primary T cells from cord blood	blood
30	chr6:5652800-5655000	Strong transcription	Fetal Stomach	stomach
31	chr6:5653200-5656400	Weak transcription	Primary B cells from cord blood	blood
32	chr6:5653200-5659200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr6:5653200-5660400	Weak transcription	Ovary	ovary
34	chr6:5653200-5677600	Weak transcription	Gastric	stomach
35	chr6:5653400-5656000	Weak transcription	NHEK	skin
36	chr6:5654200-5657600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr6:5654600-5671400	Weak transcription	Left Ventricle	heart
38	chr6:5654600-5677600	Weak transcription	Pancreas	Pancrea

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