Variant report

Variant	rs17741826
Chromosome Location	chr5:151149262-151149263
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:151148547-151149867	HepG2	liver:	n/a	n/a
2	POLR2A	chr5:151148595-151149407	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr5:151148376-151153894	K562	blood:	n/a	n/a
4	POLR2A	chr5:151148530-151149388	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr5:151149017-151153094	Hela-S3	cervix:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:151141912..151146351-chr5:151146659..151152863,9	MCF-7	breast:
2	chr5:150861725..150863325-chr5:151147345..151150337,2	K562	blood:
3	chr5:151133870..151141079-chr5:151148554..151154544,14	MCF-7	breast:
4	chr5:151146976..151149918-chr5:151242837..151245370,2	K562	blood:
5	chr5:151136180..151141661-chr5:151146894..151154161,25	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GLRA1-1	chr5:151149191-151150353	NONHSAT104635

No data

Variant related genes	Relation type
G3BP1	TF binding region
ENSG00000213433	TF binding region
ENSG00000177556	Chromatin interaction
ENSG00000213433	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10044368	0.94[CHB][hapmap]
rs1042877	0.94[CHB][hapmap]
rs1062177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875569	0.81[ASN][1000 genomes]
rs12108921	0.87[CHB][hapmap]
rs12109022	0.88[CHB][hapmap]
rs12515762	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12522670	0.85[CEU][hapmap]
rs12654573	0.86[EUR][1000 genomes]
rs1433041	0.94[CHB][hapmap]
rs1549920	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1549921	0.81[ASN][1000 genomes]
rs177349	1.00[YRI][hapmap]
rs17804178	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs188553	1.00[YRI][hapmap]
rs1972780	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1978710	0.80[ASN][1000 genomes]
rs2016409	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2053063	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2347596	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2347597	0.94[CHB][hapmap]
rs2584895	1.00[YRI][hapmap]
rs2913889	0.88[CHB][hapmap]
rs2913892	0.87[CHB][hapmap]
rs2913893	0.88[CHB][hapmap]
rs2913894	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs2915815	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2915816	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2915817	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2915818	0.93[ASN][1000 genomes]
rs2915820	0.90[ASN][1000 genomes]
rs2915822	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2915826	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2915827	0.86[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2915828	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2915829	0.83[ASN][1000 genomes]
rs2915868	0.94[CHB][hapmap]
rs2915869	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2915872	0.94[CHB][hapmap]
rs2915873	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2915874	0.85[ASN][1000 genomes]
rs2915876	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915877	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915878	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915879	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2915880	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2915881	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2915882	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2915883	0.81[ASN][1000 genomes]
rs2915886	0.88[CHB][hapmap]
rs2915887	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2915888	0.94[CHB][hapmap];0.87[JPT][hapmap]
rs2915890	0.93[CHB][hapmap];0.81[JPT][hapmap]
rs2964570	0.94[CHB][hapmap]
rs2964571	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2964573	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2964574	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2964576	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2964577	0.85[ASN][1000 genomes]
rs2964578	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2964580	0.81[ASN][1000 genomes]
rs2964581	0.81[ASN][1000 genomes]
rs2964582	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2964583	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2964584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2964585	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2964587	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2964588	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2964589	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2964590	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2964591	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2964592	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2964593	0.92[ASN][1000 genomes]
rs2964594	0.84[ASN][1000 genomes]
rs2964595	0.86[ASN][1000 genomes]
rs2964612	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2964613	0.81[ASN][1000 genomes]
rs302392	1.00[YRI][hapmap]
rs302395	1.00[YRI][hapmap]
rs400545	1.00[YRI][hapmap]
rs4571461	0.94[CHB][hapmap]
rs62377931	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62377945	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6579897	1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs6579901	0.89[ASN][1000 genomes]
rs6878198	0.84[ASN][1000 genomes]
rs6890099	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72802204	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7719617	0.94[CHB][hapmap]
rs7728956	0.86[CHB][hapmap]
rs7733241	0.87[CHB][hapmap]
rs7734314	0.94[CHB][hapmap]
rs892005	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs892006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs973529	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17741826	RP11-54C4.1	cis	Nerve Tibial	GTEx
rs17741826	RP11-54C4.1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:151138800-151149600	Weak transcription	Aorta	Aorta
2	chr5:151138800-151149800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:151139200-151149600	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr5:151139400-151149800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr5:151139400-151149800	Weak transcription	Right Atrium	heart
6	chr5:151143200-151149800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr5:151145600-151150000	Weak transcription	Pancreas	Pancrea
8	chr5:151145800-151149600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:151145800-151150000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr5:151146000-151149800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr5:151147200-151149800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr5:151148600-151149600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:151148600-151149600	Enhancers	Primary B cells from cord blood	blood
14	chr5:151148600-151149800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:151148800-151149600	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr5:151148800-151149800	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr5:151148800-151149800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr5:151148800-151149800	Weak transcription	A549	lung
19	chr5:151149000-151149400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:151149000-151149600	Enhancers	Duodenum Mucosa	Duodenum
21	chr5:151149000-151149600	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr5:151149000-151149600	Enhancers	GM12878-XiMat	blood
23	chr5:151149000-151149600	Enhancers	K562	blood
24	chr5:151149000-151149800	Enhancers	Primary B cells from peripheral blood	blood
25	chr5:151149000-151149800	Enhancers	Primary T cells fromperipheralblood	blood
26	chr5:151149000-151149800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr5:151149000-151149800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr5:151149000-151150000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:151149000-151150000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr5:151149000-151150000	Enhancers	Placenta	Placenta
31	chr5:151149000-151150000	Enhancers	Spleen	Spleen
32	chr5:151149000-151153200	Active TSS	Rectal Smooth Muscle	rectum
33	chr5:151149200-151149600	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr5:151149200-151149600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr5:151149200-151149600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr5:151149200-151149600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr5:151149200-151149600	Enhancers	Brain Germinal Matrix	brain
38	chr5:151149200-151149600	Enhancers	Brain Hippocampus Middle	brain
39	chr5:151149200-151149600	Enhancers	Fetal Brain Female	brain
40	chr5:151149200-151149600	Enhancers	Small Intestine	intestine
41	chr5:151149200-151149600	Enhancers	Dnd41	blood
42	chr5:151149200-151149600	Enhancers	Hela-S3	cervix
43	chr5:151149200-151149800	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr5:151149200-151149800	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr5:151149200-151149800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr5:151149200-151149800	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr5:151149200-151149800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr5:151149200-151149800	Enhancers	Fetal Muscle Leg	muscle
49	chr5:151149200-151150000	Enhancers	Primary hematopoietic stem cells	blood
50	chr5:151149200-151150200	Enhancers	Fetal Heart	heart

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