Variant report

Variant	rs3744125
Chromosome Location	chr17:17094919-17094920
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17089905..17092856-chr17:17094714..17097551,4	K562	blood:
2	chr17:17093441..17095479-chr17:17108038..17109753,2	MCF-7	breast:
3	chr17:17092917..17095538-chr17:17100650..17103433,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C17orf84-1	chr17:17091982-17095962	ENSG00000259850.1
2	lnc-C17orf84-1	chr17:17093701-17095957	NONHSAT146066

Variant related genes	Relation type
ENSG00000179598	Chromatin interaction

Extended variants
information (count: 139 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs1047799	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1047805	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10852843	0.90[AMR][1000 genomes]
rs10852844	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10852845	0.90[AMR][1000 genomes]
rs10852846	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11078364	0.83[AMR][1000 genomes]
rs11078365	0.88[AMR][1000 genomes]
rs11078368	0.81[ASN][1000 genomes]
rs11078370	0.90[AMR][1000 genomes]
rs11078371	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11078372	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11078373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11078375	0.95[AMR][1000 genomes]
rs1110504	0.95[AMR][1000 genomes]
rs1110505	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11551189	0.91[ASN][1000 genomes]
rs11651460	0.95[AMR][1000 genomes]
rs11651938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11651988	0.90[AMR][1000 genomes]
rs11652079	0.95[AMR][1000 genomes]
rs11652678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11652756	0.90[AMR][1000 genomes]
rs11652936	0.90[AMR][1000 genomes]
rs11654247	0.95[AMR][1000 genomes]
rs11654360	0.86[AMR][1000 genomes]
rs11654562	0.88[AMR][1000 genomes]
rs11654887	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11657189	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11658084	0.90[AMR][1000 genomes]
rs11870035	0.90[ASN][1000 genomes]
rs11870483	0.80[ASN][1000 genomes]
rs12450109	0.90[AMR][1000 genomes]
rs12450213	0.88[AMR][1000 genomes]
rs12450238	0.88[AMR][1000 genomes]
rs12450467	0.90[AMR][1000 genomes]
rs12451054	0.90[AMR][1000 genomes]
rs12451343	0.80[EUR][1000 genomes]
rs12452802	0.95[AMR][1000 genomes]
rs12601325	0.95[AMR][1000 genomes]
rs12601422	0.94[CHB][hapmap]
rs12602129	0.90[AMR][1000 genomes]
rs12602583	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12602592	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12602839	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12602867	0.95[AMR][1000 genomes]
rs12603417	0.81[ASN][1000 genomes]
rs1567815	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16961288	0.90[AMR][1000 genomes]
rs16961412	0.88[AMR][1000 genomes]
rs17794784	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2292526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2292530	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2349645	0.90[ASN][1000 genomes]
rs2349648	0.80[ASN][1000 genomes]
rs34976658	0.98[ASN][1000 genomes]
rs3744127	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3744131	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3744132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3744133	0.95[AMR][1000 genomes]
rs3744134	0.94[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs3744136	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3744137	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3744138	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3744139	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3744140	0.95[AMR][1000 genomes]
rs3826305	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4073688	0.91[CEU][hapmap];0.89[CHB][hapmap]
rs4074611	0.90[AMR][1000 genomes]
rs4074612	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4074819	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4264448	0.90[AMR][1000 genomes]
rs4275916	0.90[AMR][1000 genomes]
rs4283273	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4321246	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4606773	0.90[AMR][1000 genomes]
rs4621033	0.90[AMR][1000 genomes]
rs4629023	0.91[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4985695	0.90[AMR][1000 genomes]
rs4985697	0.90[AMR][1000 genomes]
rs4985698	0.90[AMR][1000 genomes]
rs4985703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4985704	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4985714	0.90[AMR][1000 genomes]
rs4985716	0.80[EUR][1000 genomes]
rs4985719	0.90[AMR][1000 genomes]
rs4985727	0.90[AMR][1000 genomes]
rs4985728	0.81[ASN][1000 genomes]
rs4985730	0.80[ASN][1000 genomes]
rs4985737	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs4985739	0.95[AMR][1000 genomes]
rs4985741	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4985742	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985743	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4985744	0.95[AMR][1000 genomes]
rs4985745	0.94[ASN][1000 genomes]
rs4985747	0.90[AMR][1000 genomes]
rs55751545	0.95[AMR][1000 genomes]
rs56009207	0.90[AMR][1000 genomes]
rs56133536	0.90[ASN][1000 genomes]
rs57812549	0.93[AMR][1000 genomes]
rs58326998	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58472573	0.90[AMR][1000 genomes]
rs58814183	0.90[AMR][1000 genomes]
rs59394251	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60128647	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61018209	0.95[AMR][1000 genomes]
rs7207187	0.90[AMR][1000 genomes]
rs7210339	0.90[AMR][1000 genomes]
rs7211576	0.98[ASN][1000 genomes]
rs7212275	0.80[EUR][1000 genomes]
rs7214429	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7216677	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7217970	0.95[AMR][1000 genomes]
rs7218781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs7223583	0.90[AMR][1000 genomes]
rs73979053	0.83[AMR][1000 genomes]
rs73979054	0.90[AMR][1000 genomes]
rs73979058	0.90[AMR][1000 genomes]
rs73979060	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73979061	0.90[AMR][1000 genomes]
rs73979078	0.81[ASN][1000 genomes]
rs73979081	0.90[AMR][1000 genomes]
rs73979082	0.90[AMR][1000 genomes]
rs73979083	0.90[AMR][1000 genomes]
rs8064991	0.95[AMR][1000 genomes]
rs8066111	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8066234	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs8067563	0.90[AMR][1000 genomes]
rs8069259	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8071254	0.80[EUR][1000 genomes]
rs8076273	0.84[CHB][hapmap]
rs8077360	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9893676	0.91[ASN][1000 genomes]
rs9895060	0.85[ASN][1000 genomes]
rs9897510	0.91[ASN][1000 genomes]
rs9910857	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv907728	chr17:17013189-17095487	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv833380	chr17:17088416-17241206	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3744125	LOC201164	Cis_1M	lymphoblastoid	RTeQTL
rs3744125	M-RIP	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17056800-17095000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr17:17076600-17104600	Weak transcription	K562	blood
3	chr17:17084400-17095200	Weak transcription	Fetal Kidney	kidney
4	chr17:17086400-17095200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr17:17086400-17104800	Weak transcription	Brain Substantia Nigra	brain
6	chr17:17086400-17106600	Weak transcription	Colonic Mucosa	Colon
7	chr17:17087600-17095400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr17:17089400-17095200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr17:17089600-17096600	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr17:17090200-17107000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr17:17090200-17107400	Weak transcription	Small Intestine	intestine
12	chr17:17090600-17095600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr17:17090800-17106600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr17:17090800-17106600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr17:17090800-17107200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr17:17091200-17104400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr17:17091400-17095200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr17:17091400-17104000	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr17:17091800-17107600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr17:17092200-17095200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr17:17092200-17095200	Weak transcription	Brain Hippocampus Middle	brain
22	chr17:17092200-17105400	Weak transcription	Gastric	stomach
23	chr17:17092400-17095400	Weak transcription	GM12878-XiMat	blood
24	chr17:17092400-17104200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr17:17092400-17105600	Weak transcription	Brain Germinal Matrix	brain
26	chr17:17092600-17095200	Weak transcription	Fetal Intestine Large	intestine
27	chr17:17092800-17095600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr17:17092800-17096200	Enhancers	Colon Smooth Muscle	Colon
29	chr17:17093000-17095000	Genic enhancers	NHEK	skin
30	chr17:17093000-17095200	Enhancers	Spleen	Spleen
31	chr17:17093000-17095400	Enhancers	Rectal Smooth Muscle	rectum
32	chr17:17093000-17095600	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr17:17093000-17104800	Weak transcription	Hela-S3	cervix
34	chr17:17093200-17095600	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr17:17093200-17095600	Enhancers	Left Ventricle	heart
36	chr17:17093200-17095600	Genic enhancers	A549	lung
37	chr17:17093200-17095600	Enhancers	NH-A	brain
38	chr17:17093200-17095800	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr17:17093400-17095000	Enhancers	Right Ventricle	heart
40	chr17:17093400-17095600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr17:17093400-17095600	Enhancers	Stomach Smooth Muscle	stomach
42	chr17:17093400-17096200	Enhancers	NHLF	lung
43	chr17:17093600-17095600	Enhancers	NHDF-Ad	bronchial
44	chr17:17093600-17102400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr17:17093600-17103400	Weak transcription	Fetal Thymus	thymus
46	chr17:17093600-17104400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr17:17093600-17107400	Weak transcription	Dnd41	blood
48	chr17:17093600-17108400	Weak transcription	Thymus	Thymus
49	chr17:17093800-17095000	Enhancers	HSMMtube	muscle
50	chr17:17093800-17095200	Weak transcription	Primary T helper cells PMA-I stimulated	--

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