Variant report

Variant	rs12939739
Chromosome Location	chr17:46003188-46003189
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:45973265..45977043-chr17:45998491..46003792,7	MCF-7	breast:
2	chr17:45974878..45977034-chr17:46001885..46004238,2	K562	blood:
3	chr17:45998420..46000052-chr17:46002158..46004611,2	K562	blood:

Variant related genes	Relation type
ENSG00000167182	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10459927	0.84[ASN][1000 genomes]
rs11079801	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11079803	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1108833	0.90[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs1130932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11652185	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11652827	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11655068	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11655352	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11659126	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11870852	0.86[ASN][1000 genomes]
rs12601827	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12602494	0.85[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs13353189	0.85[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap]
rs2228251	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2228253	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2229358	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2318118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2325747	0.89[ASN][1000 genomes]
rs2325751	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2525107	0.81[ASN][1000 genomes]
rs3096	0.85[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs34593510	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35280206	0.85[ASN][1000 genomes]
rs36124074	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764396	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4369725	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4793731	0.85[ASN][1000 genomes]
rs4793732	0.81[ASN][1000 genomes]
rs4793733	0.85[CHB][hapmap];0.93[JPT][hapmap];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	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67194241	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7208707	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7211859	0.90[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs72840237	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8066893	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8071003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9895863	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9903223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12939739	RP11-6N17.4	cis	Skin Sun Exposed Lower leg	GTEx
rs12939739	SP2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45980200-46006400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr17:45983000-46004000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr17:45983200-46018200	Weak transcription	Fetal Brain Male	brain
4	chr17:45991800-46006400	Strong transcription	Fetal Stomach	stomach
5	chr17:45992400-46008400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr17:45993800-46017400	Weak transcription	Psoas Muscle	Psoas
7	chr17:45994000-46013200	Weak transcription	Fetal Heart	heart
8	chr17:45994200-46006000	Strong transcription	Fetal Muscle Trunk	muscle
9	chr17:45994400-46006000	Strong transcription	Fetal Muscle Leg	muscle
10	chr17:45995800-46012200	Weak transcription	HUVEC	blood vessel
11	chr17:45996000-46008200	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr17:45996200-46008200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr17:45996200-46012600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr17:45996600-46005000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr17:45996600-46008400	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr17:45997400-46008200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr17:45997600-46006200	Strong transcription	Fetal Intestine Small	intestine
18	chr17:45998000-46008200	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr17:45998000-46009400	Strong transcription	Fetal Thymus	thymus
20	chr17:45998200-46008000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr17:45998200-46008200	Strong transcription	Dnd41	blood
22	chr17:45998200-46008400	Strong transcription	Primary B cells from peripheral blood	blood
23	chr17:45998200-46008400	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr17:45998200-46011000	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr17:45998400-46003200	Strong transcription	GM12878-XiMat	blood
26	chr17:45998400-46005000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr17:45998400-46005200	Strong transcription	Fetal Lung	lung
28	chr17:45998400-46006000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr17:45998400-46006400	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr17:45998400-46008000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr17:45998400-46008200	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr17:45998800-46006400	Strong transcription	Duodenum Mucosa	Duodenum
33	chr17:45998800-46008400	Strong transcription	Spleen	Spleen
34	chr17:45998800-46009600	Strong transcription	Placenta	Placenta
35	chr17:45999000-46005200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
36	chr17:45999000-46005600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr17:45999000-46005800	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr17:45999000-46006600	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr17:45999000-46008000	Strong transcription	Fetal Intestine Large	intestine
40	chr17:45999000-46008000	Strong transcription	Thymus	Thymus
41	chr17:45999000-46008200	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr17:45999000-46008200	Strong transcription	Ovary	ovary
43	chr17:45999000-46008400	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr17:45999000-46008400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr17:45999000-46008400	Strong transcription	Fetal Brain Female	brain
46	chr17:45999000-46009600	Strong transcription	Primary T cells from cord blood	blood
47	chr17:45999000-46010400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr17:45999200-46008200	Strong transcription	Primary B cells from cord blood	blood
49	chr17:45999200-46008400	Strong transcription	Brain Germinal Matrix	brain
50	chr17:45999200-46018200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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