Variant report

Variant	rs34593510
Chromosome Location	chr17:46001535-46001536
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46000951..46003087-chr17:46034004..46036167,2	K562	blood:
2	chr17:45920864..45922757-chr17:46000499..46002705,2	K562	blood:
3	chr17:45973265..45977043-chr17:45998491..46003792,7	MCF-7	breast:
4	chr17:45999369..46002049-chr17:46009098..46012075,3	MCF-7	breast:
5	chr17:46000022..46002269-chr17:46003613..46007289,3	MCF-7	breast:
6	chr17:45989573..45991691-chr17:45999240..46001944,2	K562	blood:
7	chr17:45999533..46002331-chr17:46009358..46011898,2	K562	blood:

Variant related genes	Relation type
ENSG00000167183	Chromatin interaction
ENSG00000167182	Chromatin interaction
ENSG00000266601	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10459927	0.84[ASN][1000 genomes]
rs11079801	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11079803	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1108833	0.86[ASN][1000 genomes]
rs1130932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11652185	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11652827	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11655068	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11655352	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11659126	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11870852	0.86[ASN][1000 genomes]
rs12601827	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12602494	0.85[ASN][1000 genomes]
rs12939739	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2228251	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2228253	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2229358	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2318118	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2325747	0.89[ASN][1000 genomes]
rs2325751	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2525107	0.81[ASN][1000 genomes]
rs3096	0.85[ASN][1000 genomes]
rs35280206	0.85[ASN][1000 genomes]
rs36124074	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764396	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4369725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4793731	0.85[ASN][1000 genomes]
rs4793732	0.81[ASN][1000 genomes]
rs4793733	0.85[ASN][1000 genomes]
rs4793737	0.85[ASN][1000 genomes]
rs4794261	0.86[ASN][1000 genomes]
rs4794286	0.89[ASN][1000 genomes]
rs4794332	0.85[ASN][1000 genomes]
rs6503934	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67194241	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7208707	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7211859	0.86[ASN][1000 genomes]
rs72840237	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8066893	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8071003	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9895863	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9903223	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv2072	chr17:45998637-46019626	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs34593510	SP2	Cis_1M	lymphoblastoid	RTeQTL
rs34593510	RP11-6N17.4	cis	Muscle Skeletal	GTEx
rs34593510	RP11-6N17.4	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45980200-46001800	Weak transcription	K562	blood
2	chr17:45980200-46002400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr17:45980200-46006400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr17:45983000-46004000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr17:45983200-46018200	Weak transcription	Fetal Brain Male	brain
6	chr17:45991800-46006400	Strong transcription	Fetal Stomach	stomach
7	chr17:45992400-46008400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr17:45993800-46017400	Weak transcription	Psoas Muscle	Psoas
9	chr17:45994000-46013200	Weak transcription	Fetal Heart	heart
10	chr17:45994200-46006000	Strong transcription	Fetal Muscle Trunk	muscle
11	chr17:45994400-46002400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr17:45994400-46006000	Strong transcription	Fetal Muscle Leg	muscle
13	chr17:45994800-46002400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr17:45995800-46012200	Weak transcription	HUVEC	blood vessel
15	chr17:45996000-46008200	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr17:45996200-46008200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr17:45996200-46012600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr17:45996600-46005000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr17:45996600-46008400	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr17:45997400-46008200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr17:45997600-46006200	Strong transcription	Fetal Intestine Small	intestine
22	chr17:45998000-46008200	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr17:45998000-46009400	Strong transcription	Fetal Thymus	thymus
24	chr17:45998200-46008000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr17:45998200-46008200	Strong transcription	Dnd41	blood
26	chr17:45998200-46008400	Strong transcription	Primary B cells from peripheral blood	blood
27	chr17:45998200-46008400	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr17:45998200-46011000	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr17:45998400-46003200	Strong transcription	GM12878-XiMat	blood
30	chr17:45998400-46005000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr17:45998400-46005200	Strong transcription	Fetal Lung	lung
32	chr17:45998400-46006000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr17:45998400-46006400	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr17:45998400-46008000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr17:45998400-46008200	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr17:45998800-46006400	Strong transcription	Duodenum Mucosa	Duodenum
37	chr17:45998800-46008400	Strong transcription	Spleen	Spleen
38	chr17:45998800-46009600	Strong transcription	Placenta	Placenta
39	chr17:45999000-46005200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
40	chr17:45999000-46005600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr17:45999000-46005800	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr17:45999000-46006600	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr17:45999000-46008000	Strong transcription	Fetal Intestine Large	intestine
44	chr17:45999000-46008000	Strong transcription	Thymus	Thymus
45	chr17:45999000-46008200	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr17:45999000-46008200	Strong transcription	Ovary	ovary
47	chr17:45999000-46008400	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr17:45999000-46008400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr17:45999000-46008400	Strong transcription	Fetal Brain Female	brain
50	chr17:45999000-46009600	Strong transcription	Primary T cells from cord blood	blood

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