Variant report

Variant	rs2924257
Chromosome Location	chr17:46317555-46317556
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:46297106..46299092-chr17:46317071..46320031,2	K562	blood:
2	chr17:46304702..46306804-chr17:46316986..46319945,3	K562	blood:
3	chr17:46317007..46319839-chr17:46328201..46331501,3	K562	blood:
4	chr17:46312738..46316050-chr17:46317088..46320426,4	K562	blood:
5	chr17:46316932..46321831-chr17:46322420..46326261,9	K562	blood:
6	chr17:46297106..46299092-chr17:46317071..46320404,3	K562	blood:
7	chr17:46237804..46239741-chr17:46316113..46318637,2	MCF-7	breast:
8	chr17:46260519..46263689-chr17:46315938..46318852,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000263787	Chromatin interaction
ENSG00000141293	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12603115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12603380	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12947089	0.90[CEU][hapmap];0.86[CHB][hapmap]
rs12952670	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1316657	0.90[CEU][hapmap];0.86[CHB][hapmap]
rs1377201	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1452666	0.91[CEU][hapmap];0.86[CHB][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1452667	0.90[CEU][hapmap];0.86[CHB][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17620033	0.90[CEU][hapmap];0.86[CHB][hapmap]
rs1860862	0.90[CEU][hapmap];0.86[CHB][hapmap]
rs2021752	0.90[CEU][hapmap];0.86[CHB][hapmap]
rs2041572	0.91[CEU][hapmap];0.86[CHB][hapmap]
rs2060876	0.91[CEU][hapmap];0.86[CHB][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2072441	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs2109982	0.91[CEU][hapmap];0.86[CHB][hapmap]
rs2123341	0.90[CEU][hapmap];0.86[CHB][hapmap]
rs2278868	0.90[CEU][hapmap];0.86[CHB][hapmap]
rs2305433	0.90[CEU][hapmap];0.86[CHB][hapmap]
rs2938483	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3792692	0.90[CEU][hapmap];0.86[CHB][hapmap]
rs3792694	0.90[CEU][hapmap];0.86[CHB][hapmap]
rs3805370	0.90[CEU][hapmap];0.85[CHB][hapmap]
rs3897986	0.90[CEU][hapmap];0.86[CHB][hapmap]
rs4793779	0.91[CEU][hapmap];0.92[CHB][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4794447	0.86[CHB][hapmap]
rs4794525	0.80[EUR][1000 genomes]
rs6504108	0.86[CHB][hapmap]
rs7220768	0.85[CEU][hapmap];0.86[CHB][hapmap]
rs7223867	0.91[CEU][hapmap];0.86[CHB][hapmap]
rs7225550	0.91[CEU][hapmap];0.86[CHB][hapmap]
rs758999	0.91[CEU][hapmap];0.86[CHB][hapmap]
rs8069263	0.91[CEU][hapmap];0.86[CHB][hapmap]
rs8072282	0.90[CEU][hapmap];0.86[CHB][hapmap]
rs954226	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2924257	SNX11	cis	multi-tissue	Pritchard

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46266800-46318200	Weak transcription	Primary B cells from peripheral blood	blood
2	chr17:46294000-46318000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr17:46305200-46317600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr17:46306600-46335400	Weak transcription	Thymus	Thymus
5	chr17:46312800-46318800	Enhancers	HUVEC	blood vessel
6	chr17:46313000-46318000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr17:46314000-46318000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr17:46314000-46318200	Enhancers	NHDF-Ad	bronchial
9	chr17:46314200-46320200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr17:46315000-46317600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr17:46315000-46317800	Weak transcription	Hela-S3	cervix
12	chr17:46315000-46318000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr17:46315000-46318000	Enhancers	A549	lung
14	chr17:46315200-46317600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr17:46315200-46317800	Weak transcription	Primary T cells from cord blood	blood
16	chr17:46315200-46317800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr17:46315200-46317800	Weak transcription	NHLF	lung
18	chr17:46315200-46318000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr17:46315200-46319400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr17:46315400-46317600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr17:46315600-46317800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr17:46315800-46319600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr17:46315800-46319600	Enhancers	HMEC	breast
24	chr17:46315800-46319800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr17:46315800-46319800	Enhancers	HSMM	muscle
26	chr17:46315800-46319800	Enhancers	Osteobl	bone
27	chr17:46315800-46323000	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr17:46316000-46317600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr17:46316000-46318600	Weak transcription	Right Atrium	heart
30	chr17:46316400-46317600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr17:46316400-46318000	Enhancers	NHEK	skin
32	chr17:46316400-46319600	Enhancers	NH-A	brain
33	chr17:46316400-46322800	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr17:46316400-46324600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr17:46316600-46317800	Enhancers	K562	blood
36	chr17:46316600-46319800	Enhancers	Fetal Muscle Leg	muscle
37	chr17:46316600-46320200	Enhancers	Fetal Kidney	kidney
38	chr17:46316600-46320600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr17:46316800-46317800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr17:46316800-46318000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr17:46316800-46318000	Enhancers	GM12878-XiMat	blood
42	chr17:46317000-46319000	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr17:46317200-46317600	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr17:46317200-46318800	Enhancers	Colon Smooth Muscle	Colon
45	chr17:46317200-46319000	Enhancers	HSMMtube	muscle
46	chr17:46317200-46320000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr17:46317200-46320200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr17:46317200-46322600	Enhancers	Fetal Intestine Small	intestine
49	chr17:46317200-46324000	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr17:46317400-46318600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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