Variant report

Variant	rs13213141
Chromosome Location	chr6:64295122-64295123
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:64289729..64291970-chr6:64293483..64297039,3	MCF-7	breast:
2	chr6:64293183..64295543-chr6:64317840..64319862,2	K562	blood:
3	chr6:64288992..64292789-chr6:64292911..64296386,5	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10943869	0.80[CEU][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs12523702	0.92[MEX][hapmap];0.86[TSI][hapmap]
rs13191932	0.83[EUR][1000 genomes]
rs13205487	0.83[EUR][1000 genomes]
rs17396843	1.00[YRI][hapmap]
rs1744134	0.80[GIH][hapmap];0.83[LWK][hapmap];0.80[MEX][hapmap];0.83[YRI][hapmap]
rs1857565	0.88[YRI][hapmap]
rs2025178	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2622277	0.88[YRI][hapmap]
rs2627797	0.93[LWK][hapmap];0.94[YRI][hapmap]
rs3800489	0.83[GIH][hapmap]
rs3800490	0.83[GIH][hapmap];0.87[LWK][hapmap]
rs4351235	0.83[GIH][hapmap]
rs6916092	0.82[EUR][1000 genomes]
rs7753325	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13213141	LGSN	cis	Whole Blood	GTEx

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:64284000-64297200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:64284400-64296200	Weak transcription	Ovary	ovary
3	chr6:64284800-64307600	Weak transcription	Fetal Stomach	stomach
4	chr6:64285600-64295800	Weak transcription	Fetal Intestine Small	intestine
5	chr6:64290200-64295400	Weak transcription	Esophagus	oesophagus
6	chr6:64290200-64299200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:64290400-64296200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr6:64290400-64296600	Weak transcription	Thymus	Thymus
9	chr6:64290400-64298200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:64290400-64307600	Weak transcription	Brain Angular Gyrus	brain
11	chr6:64290400-64307600	Weak transcription	Brain Substantia Nigra	brain
12	chr6:64290600-64299200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr6:64290600-64299600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr6:64290600-64300000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr6:64290600-64300400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:64290600-64302600	Weak transcription	Fetal Brain Male	brain
17	chr6:64290600-64307600	Weak transcription	Colon Smooth Muscle	Colon
18	chr6:64290800-64296400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr6:64290800-64296600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr6:64290800-64298400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr6:64290800-64299800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr6:64291000-64295200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr6:64291000-64297000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:64291000-64298200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr6:64291200-64296400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr6:64291200-64299800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr6:64291200-64307600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr6:64291400-64295600	Weak transcription	Brain Hippocampus Middle	brain
29	chr6:64291400-64307800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr6:64291600-64299800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr6:64291600-64299800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr6:64291800-64295400	Weak transcription	NHDF-Ad	bronchial
33	chr6:64291800-64299800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr6:64291800-64307600	Weak transcription	Fetal Brain Female	brain
35	chr6:64292000-64299400	Weak transcription	HepG2	liver
36	chr6:64292200-64299800	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr6:64292800-64295200	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr6:64292800-64295200	Weak transcription	HUVEC	blood vessel
39	chr6:64292800-64296000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr6:64292800-64299600	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr6:64292800-64299600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr6:64292800-64300000	Weak transcription	Hela-S3	cervix
43	chr6:64293000-64295400	Weak transcription	Primary B cells from peripheral blood	blood
44	chr6:64293000-64295400	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr6:64293000-64295600	Weak transcription	NHEK	skin
46	chr6:64293000-64296200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr6:64293000-64296600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr6:64293000-64297000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr6:64293000-64297000	Weak transcription	GM12878-XiMat	blood
50	chr6:64293000-64298600	Weak transcription	Primary neutrophils fromperipheralblood	blood

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