Variant report

Variant	rs6890099
Chromosome Location	chr5:151151962-151151963
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:151150059-151152517	NB4	blood:	n/a	n/a
2	SMARCB1	chr5:151149958-151152619	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr5:151151854-151152660	U87	brain:	n/a	n/a
4	POLR2A	chr5:151150162-151152760	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr5:151151331-151151979	A549	lung:	n/a	n/a
6	RELA	chr5:151150562-151152188	GM19193	blood:	n/a	n/a
7	POLR2A	chr5:151151273-151152736	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr5:151149886-151152833	HL-60	blood:	n/a	n/a
9	HEY1	chr5:151150086-151153051	K562	blood:	n/a	chr5:151150092-151150107 chr5:151151682-151151697
10	SIN3AK20	chr5:151151939-151152122	HepG2	liver:	n/a	n/a
11	SP1	chr5:151150316-151152298	HCT-116	colon:	n/a	chr5:151151606-151151620 chr5:151151610-151151619 chr5:151151609-151151621 chr5:151151616-151151625 chr5:151151610-151151620 chr5:151151611-151151620 chr5:151150447-151150461 chr5:151151609-151151621 chr5:151151042-151151063 chr5:151151610-151151620
12	TFAP2A	chr5:151149990-151152551	Hela-S3	cervix:	n/a	chr5:151150971-151150983 chr5:151150971-151150983 chr5:151150113-151150124 chr5:151150945-151150955 chr5:151150064-151150074 chr5:151152393-151152404 chr5:151150626-151150637 chr5:151150987-151151002 chr5:151150971-151150983 chr5:151150713-151150724 chr5:151150945-151150955 chr5:151150971-151150983 chr5:151150988-151150999 chr5:151150945-151150955 chr5:151150113-151150124 chr5:151150713-151150725 chr5:151152393-151152404
13	POLR2A	chr5:151151219-151153028	GM12891	blood:	n/a	n/a
14	POLR2A	chr5:151149699-151152902	GM19099	blood:	n/a	n/a
15	TBL1XR1	chr5:151150121-151152436	K562	blood:	n/a	n/a
16	POLR2A	chr5:151151268-151152576	ECC-1	luminal epithelium:	n/a	n/a
17	CTCF	chr5:151151755-151151974	K562	blood:	n/a	n/a
18	POLR2A	chr5:151150471-151152435	MCF-7	breast:	n/a	n/a
19	POLR2A	chr5:151149841-151152286	K562	blood:	n/a	n/a
20	HDAC2	chr5:151151390-151151969	HepG2	liver:	n/a	chr5:151151820-151151829
21	SIN3AK20	chr5:151150559-151152901	MCF-7	breast:	n/a	n/a
22	CHD2	chr5:151150231-151152572	GM12878	blood:	n/a	n/a
23	BHLHE40	chr5:151149969-151152512	K562	blood:	n/a	chr5:151151678-151151694 chr5:151151868-151151884 chr5:151150090-151150106
24	RELA	chr5:151150127-151152999	GM12891	blood:	n/a	chr5:151152670-151152679 chr5:151152670-151152679
25	FOXM1	chr5:151150237-151152693	GM12878	blood:	n/a	n/a
26	TAF1	chr5:151150135-151151998	K562	blood:	n/a	n/a
27	WRNIP1	chr5:151151946-151153029	GM12878	blood:	n/a	n/a
28	POLR2A	chr5:151150797-151153116	HepG2	liver:	n/a	n/a
29	POLR2A	chr5:151149843-151153078	GM12892	blood:	n/a	n/a
30	POLR2A	chr5:151150361-151152325	Gliobla	brain:	n/a	n/a
31	UBTF	chr5:151151404-151152370	K562	blood:	n/a	n/a
32	HMGN3	chr5:151149997-151152461	K562	blood:	n/a	n/a
33	RELA	chr5:151150062-151152821	GM18951	blood:	n/a	chr5:151152670-151152679 chr5:151152670-151152679
34	MAX	chr5:151150184-151152500	HCT-116	colon:	n/a	chr5:151151801-151151810 chr5:151151946-151151955 chr5:151151610-151151620 chr5:151151818-151151827
35	JUND	chr5:151150446-151151973	K562	blood:	n/a	chr5:151151927-151151936
36	CHD2	chr5:151150734-151152013	HepG2	liver:	n/a	n/a
37	POLR2A	chr5:151149923-151152694	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr5:151150098-151153044	HL-60	blood:	n/a	n/a
39	YY1	chr5:151150496-151152109	HepG2	liver:	n/a	chr5:151151869-151151878 chr5:151151864-151151878 chr5:151150940-151150954
40	CHD1	chr5:151151941-151153142	H1-hESC	embryonic stem cell:	n/a	n/a
41	NR3C1	chr5:151150825-151152000	A549	lung:	n/a	chr5:151151613-151151626
42	POLR2A	chr5:151149961-151153058	IMR90	lung:	n/a	n/a
43	RELA	chr5:151149948-151153037	GM15510	blood:	n/a	chr5:151152670-151152679 chr5:151152670-151152679
44	PAX5	chr5:151151341-151152050	GM12892	blood:	n/a	chr5:151151688-151151697
45	IRF1	chr5:151150205-151153107	K562	blood:	n/a	chr5:151151609-151151623 chr5:151151221-151151230
46	POLR2A	chr5:151149638-151153076	GM12878	blood:	n/a	n/a
47	MYC	chr5:151150216-151152462	K562	blood:	n/a	chr5:151151801-151151810 chr5:151151946-151151955 chr5:151151610-151151620 chr5:151151818-151151827
48	POLR2A	chr5:151150234-151152615	H1-neurons	neurons:	n/a	n/a
49	TBL1XR1	chr5:151150197-151152211	GM12878	blood:	n/a	n/a
50	SIN3A	chr5:151150051-151153099	H1-hESC	embryonic stem cell:	n/a	chr5:151151546-151151560 chr5:151151582-151151593 chr5:151150643-151150652

No.	Distal block	Cell Line	Cell type
1	chr5:151141912..151146351-chr5:151146659..151152863,9	MCF-7	breast:
2	chr5:151064445..151066253-chr5:151150599..151153254,2	MCF-7	breast:
3	chr15:65596704..65597315-chr5:151151434..151151998,2	Hela-S3	cervix:
4	chr2:160568928..160569499-chr5:151151506..151152069,2	Hela-S3	cervix:
5	chr5:151151845..151152390-chr6:13574797..13575459,2	Hela-S3	cervix:
6	chr5:151133870..151141079-chr5:151148554..151154544,14	MCF-7	breast:
7	chr11:31390804..31391716-chr5:151151366..151151972,2	Hela-S3	cervix:
8	chr11:62606645..62607642-chr5:151151456..151152199,2	Hela-S3	cervix:
9	chr1:229761845..229762408-chr5:151151154..151152089,2	Hela-S3	cervix:
10	chr17:35766980..35767501-chr5:151151185..151151972,2	Hela-S3	cervix:
11	chr1:40505475..40505993-chr5:151151452..151151980,2	Hela-S3	cervix:
12	chr5:151136180..151141661-chr5:151146894..151154161,25	MCF-7	breast:
13	chr17:71307281..71307838-chr5:151151478..151152013,2	Hela-S3	cervix:

Variant related genes	Relation type
G3BP1	TF binding region
ENSG00000170959	Chromatin interaction
ENSG00000213433	Chromatin interaction
ENSG00000108264	Chromatin interaction
ENSG00000135763	Chromatin interaction
ENSG00000200156	Chromatin interaction
ENSG00000179604	Chromatin interaction
ENSG00000131236	Chromatin interaction
ENSG00000170946	Chromatin interaction
ENSG00000124523	Chromatin interaction
ENSG00000113140	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000136536	Chromatin interaction
ENSG00000226266	Chromatin interaction
ENSG00000177556	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1062177	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12515762	0.86[EUR][1000 genomes]
rs12654573	0.84[EUR][1000 genomes]
rs1549920	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17741826	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17804178	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1972780	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2016409	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2053063	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2347596	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2915815	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2915816	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2915817	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2915818	0.90[ASN][1000 genomes]
rs2915820	0.87[ASN][1000 genomes]
rs2915822	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2915826	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2915827	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2915828	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2915829	0.80[ASN][1000 genomes]
rs2915869	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2915873	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2915874	0.82[ASN][1000 genomes]
rs2915876	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2915877	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2915878	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2915879	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2915880	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2915881	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2915882	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2915887	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2964571	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2964573	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2964574	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2964576	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2964577	0.82[ASN][1000 genomes]
rs2964578	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2964582	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2964583	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2964584	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2964585	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2964587	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2964588	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2964589	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2964590	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2964591	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2964592	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2964593	0.89[ASN][1000 genomes]
rs2964594	0.84[ASN][1000 genomes]
rs2964595	0.83[ASN][1000 genomes]
rs2964612	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62377931	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62377945	0.86[EUR][1000 genomes]
rs6579897	0.83[ASN][1000 genomes]
rs6579901	0.86[ASN][1000 genomes]
rs6878198	0.80[ASN][1000 genomes]
rs72802204	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs892005	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs892006	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs973529	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6890099	RP11-54C4.1	cis	Nerve Tibial	GTEx
rs6890099	RP11-54C4.1	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:151149000-151153200	Active TSS	Rectal Smooth Muscle	rectum
2	chr5:151149600-151152800	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr5:151149600-151152800	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr5:151149600-151153000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:151149600-151153600	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr5:151149600-151153600	Active TSS	H9 Cell Line	embryonic stem cell
7	chr5:151149600-151153600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:151149600-151153600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr5:151149600-151154400	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr5:151149600-151155000	Active TSS	Psoas Muscle	Psoas
11	chr5:151149800-151152000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:151149800-151152600	Active TSS	K562	blood
13	chr5:151149800-151152800	Active TSS	Brain Substantia Nigra	brain
14	chr5:151149800-151152800	Active TSS	Fetal Brain Female	brain
15	chr5:151149800-151153000	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr5:151149800-151153000	Active TSS	Colon Smooth Muscle	Colon
17	chr5:151149800-151153000	Active TSS	Esophagus	oesophagus
18	chr5:151149800-151153000	Active TSS	Left Ventricle	heart
19	chr5:151149800-151153000	Active TSS	Sigmoid Colon	Sigmoid Colon
20	chr5:151149800-151153000	Active TSS	Small Intestine	intestine
21	chr5:151149800-151153200	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr5:151149800-151153200	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr5:151149800-151153400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr5:151149800-151153400	Active TSS	Brain Angular Gyrus	brain
25	chr5:151149800-151153400	Active TSS	Fetal Intestine Large	intestine
26	chr5:151149800-151153600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr5:151149800-151154000	Active TSS	Brain Germinal Matrix	brain
28	chr5:151149800-151154400	Active TSS	H1 Cell Line	embryonic stem cell
29	chr5:151149800-151154400	Active TSS	Hela-S3	cervix
30	chr5:151149800-151154400	Active TSS	NHLF	lung
31	chr5:151149800-151154800	Active TSS	Right Ventricle	heart
32	chr5:151149800-151155000	Active TSS	Aorta	Aorta
33	chr5:151150000-151152200	Active TSS	Dnd41	blood
34	chr5:151150000-151152400	Active TSS	Liver	Liver
35	chr5:151150000-151152400	Active TSS	Brain Cingulate Gyrus	brain
36	chr5:151150000-151152800	Active TSS	Brain Anterior Caudate	brain
37	chr5:151150000-151152800	Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr5:151150000-151153000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr5:151150000-151153000	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr5:151150000-151153000	Active TSS	Gastric	stomach
41	chr5:151150000-151153000	Active TSS	Lung	lung
42	chr5:151150000-151153200	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr5:151150000-151153200	Active TSS	Duodenum Mucosa	Duodenum
44	chr5:151150000-151153400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr5:151150000-151153400	Active TSS	Fetal Stomach	stomach
46	chr5:151150000-151153600	Active TSS	Ovary	ovary
47	chr5:151150000-151154000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr5:151150000-151154400	Active TSS	Fetal Kidney	kidney
49	chr5:151150000-151154400	Active TSS	GM12878-XiMat	blood
50	chr5:151150200-151152000	Weak transcription	Fetal Heart	heart

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