Variant report

Variant	rs1108833
Chromosome Location	chr17:45982797-45982798
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:45981397..45984686-chr17:45985250..45989369,5	K562	blood:
2	chr17:45980692..45982810-chr17:45985460..45986987,2	MCF-7	breast:
3	chr17:45920976..45922650-chr17:45981473..45983982,2	MCF-7	breast:
4	chr17:45981911..45983503-chr17:45998627..46000923,2	K562	blood:
5	chr17:45981534..45985192-chr17:45991810..45993717,3	MCF-7	breast:
6	chr17:45982730..45985492-chr17:46018085..46020258,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234494	Chromatin interaction
ENSG00000108439	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10459927	0.91[ASN][1000 genomes]
rs11079801	0.90[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs11079803	0.90[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs11079804	0.84[CHB][hapmap]
rs1130932	0.90[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs11652185	0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs11652827	0.86[ASN][1000 genomes]
rs11654010	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11655068	0.84[ASN][1000 genomes]
rs11655352	0.84[ASN][1000 genomes]
rs11659126	0.86[ASN][1000 genomes]
rs11870852	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12601827	0.83[ASN][1000 genomes]
rs12602494	0.84[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap]
rs12939739	0.90[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs13353189	0.84[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs17616603	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17617250	0.89[CHB][hapmap]
rs2228251	0.90[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs2228253	0.90[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs2229358	0.90[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs2318118	0.90[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs2325747	0.96[ASN][1000 genomes]
rs2325749	0.82[AMR][1000 genomes]
rs2325751	0.90[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs3096	0.83[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap]
rs34064155	0.82[ASN][1000 genomes]
rs34593510	0.86[ASN][1000 genomes]
rs35336840	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36124074	0.86[ASN][1000 genomes]
rs3764396	0.90[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs4369725	0.85[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs4793733	0.83[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap]
rs4794261	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4794286	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6503934	0.90[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs67194241	0.86[ASN][1000 genomes]
rs7208707	0.90[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs7211859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72840237	0.84[ASN][1000 genomes]
rs8066893	0.84[ASN][1000 genomes]
rs8071003	0.86[ASN][1000 genomes]
rs9895863	0.90[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs9903223	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
4	nsv1062503	chr17:45977445-46021384	Strong transcription Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1108833	SKAP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45974200-45982800	Weak transcription	Spleen	Spleen
2	chr17:45974600-45992000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr17:45975000-45982800	Weak transcription	Gastric	stomach
4	chr17:45975000-45993400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr17:45975200-45999400	Weak transcription	Fetal Kidney	kidney
6	chr17:45975200-46000400	Weak transcription	Small Intestine	intestine
7	chr17:45975400-45983000	Weak transcription	HUVEC	blood vessel
8	chr17:45975600-45992800	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr17:45975800-46000600	Weak transcription	Hela-S3	cervix
10	chr17:45976400-45983000	Weak transcription	Aorta	Aorta
11	chr17:45976400-45993200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr17:45976400-45995400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr17:45976800-45983000	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr17:45976800-45987000	Strong transcription	Fetal Intestine Small	intestine
15	chr17:45977000-45984000	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr17:45977200-45984800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr17:45977600-45982800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr17:45977600-45992800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr17:45977600-45995000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr17:45977800-45992000	Weak transcription	Dnd41	blood
21	chr17:45977800-45992600	Weak transcription	Fetal Intestine Large	intestine
22	chr17:45977800-45992600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr17:45977800-45992800	Weak transcription	GM12878-XiMat	blood
24	chr17:45978000-45982800	Weak transcription	Fetal Brain Female	brain
25	chr17:45978400-45985000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr17:45978800-45985200	Enhancers	Psoas Muscle	Psoas
27	chr17:45979200-45987400	Weak transcription	Thymus	Thymus
28	chr17:45979400-45983800	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr17:45979400-45984600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr17:45979600-45983200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr17:45979600-45984600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr17:45979800-46000400	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr17:45980000-45992600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr17:45980000-45992800	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr17:45980000-45992800	Weak transcription	Brain Germinal Matrix	brain
36	chr17:45980200-45986000	Enhancers	Fetal Muscle Trunk	muscle
37	chr17:45980200-46001800	Weak transcription	K562	blood
38	chr17:45980200-46002400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr17:45980200-46006400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr17:45980400-45992400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr17:45980400-45993600	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr17:45980800-45983000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr17:45980800-45987000	Enhancers	Left Ventricle	heart
44	chr17:45980800-45992600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr17:45981200-45984000	Genic enhancers	Fetal Muscle Leg	muscle
46	chr17:45981400-45985000	Enhancers	Right Atrium	heart
47	chr17:45981600-45982800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr17:45981600-45982800	Enhancers	Rectal Smooth Muscle	rectum
49	chr17:45981600-45983000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr17:45981600-45983000	Enhancers	Liver	Liver

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