Variant report

Variant	rs960499
Chromosome Location	chr5:154136016-154136017
allele	C/T
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	ZBTB7A	chr5:154134805-154136152	K562	blood:	n/a	n/a
2	E2F6	chr5:154135783-154136090	K562	blood:	n/a	n/a
3	TCF12	chr5:154133420-154136643	A549	lung:	n/a	chr5:154133494-154133502 chr5:154134317-154134324
4	ELK1	chr5:154135552-154136126	Hela-S3	cervix:	n/a	n/a
5	MYC	chr5:154133822-154136192	K562	blood:	n/a	chr5:154134523-154134532 chr5:154134538-154134548 chr5:154134657-154134668 chr5:154134656-154134669 chr5:154134650-154134659 chr5:154134657-154134668 chr5:154134658-154134667
6	SIN3AK20	chr5:154134213-154137170	PANC-1	pancreas:	n/a	n/a
7	NR2F2	chr5:154135671-154136552	K562	blood:	n/a	n/a
8	MAX	chr5:154135978-154137012	SK-N-SH	brain:	n/a	chr5:154136511-154136521 chr5:154136963-154136973 chr5:154136730-154136740
9	BHLHE40	chr5:154135749-154137241	K562	blood:	n/a	n/a
10	POLR2A	chr5:154133143-154136943	K562	blood:	n/a	n/a
11	MAX	chr5:154135572-154137234	A549	lung:	n/a	chr5:154136511-154136521 chr5:154136963-154136973 chr5:154136730-154136740
12	JUND	chr5:154135167-154137237	K562	blood:	n/a	chr5:154135300-154135309 chr5:154135301-154135310 chr5:154136541-154136550 chr5:154136802-154136816
13	UBTF	chr5:154134102-154136984	K562	blood:	n/a	n/a
14	CHD1	chr5:154134917-154137347	GM12878	blood:	n/a	n/a
15	YY1	chr5:154135088-154136181	K562	blood:	n/a	chr5:154135832-154135846 chr5:154135945-154135959
16	POLR2A	chr5:154133745-154137338	PANC-1	pancreas:	n/a	n/a
17	POLR2A	chr5:154134782-154137071	GM12878	blood:	n/a	n/a
18	MYC	chr5:154134079-154136080	Hela-S3	cervix:	n/a	chr5:154134523-154134532 chr5:154134538-154134548 chr5:154134657-154134668 chr5:154134656-154134669 chr5:154134650-154134659 chr5:154134657-154134668 chr5:154134658-154134667
19	POLR2A	chr5:154134809-154137109	GM12891	blood:	n/a	n/a
20	ZNF263	chr5:154135118-154139134	HEK293-T-REx	kidney:	n/a	chr5:154136788-154136809
21	TAF1	chr5:154135671-154136118	K562	blood:	n/a	n/a
22	MAZ	chr5:154134036-154137243	GM12878	blood:	n/a	chr5:154136511-154136521 chr5:154134523-154134532 chr5:154134657-154134668 chr5:154134656-154134669 chr5:154136963-154136973 chr5:154134650-154134659 chr5:154136730-154136740 chr5:154134657-154134668 chr5:154134658-154134667
23	YY1	chr5:154134195-154136130	K562	blood:	n/a	chr5:154135832-154135846 chr5:154134391-154134400 chr5:154135945-154135959
24	HMGN3	chr5:154134186-154136077	K562	blood:	n/a	n/a
25	POLR2A	chr5:154135091-154137228	K562	blood:	n/a	n/a
26	ELF1	chr5:154133942-154137066	GM12878	blood:	n/a	chr5:154135952-154135964 chr5:154134375-154134387 chr5:154135789-154135802 chr5:154136215-154136227
27	SIN3AK20	chr5:154135463-154136410	MCF-7	breast:	n/a	n/a
28	POLR2A	chr5:154133940-154137103	K562	blood:	n/a	n/a
29	BHLHE40	chr5:154135782-154137314	GM12878	blood:	n/a	n/a
30	CTCF	chr5:154135920-154136070	SK-N-SH_RA	brain:	n/a	n/a
31	MYC	chr5:154133333-154137235	K562	blood:	n/a	chr5:154136511-154136521 chr5:154134523-154134532 chr5:154134538-154134548 chr5:154134657-154134668 chr5:154134656-154134669 chr5:154133516-154133527 chr5:154136963-154136973 chr5:154134650-154134659 chr5:154136730-154136740 chr5:154133517-154133526 chr5:154133518-154133525 chr5:154134657-154134668 chr5:154134658-154134667
32	MXI1	chr5:154132804-154137423	IMR90	lung:	n/a	n/a
33	EP300	chr5:154135923-154136021	HepG2	liver:	n/a	n/a
34	POLR2A	chr5:154133873-154137159	K562	blood:	n/a	n/a
35	POLR2A	chr5:154134224-154137029	ProgFib	skin:	n/a	n/a
36	GTF2F1	chr5:154135761-154136436	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr5:154134057-154137015	ECC-1	luminal epithelium:	n/a	n/a
38	POLR2A	chr5:154133174-154137235	Raji	blood:	n/a	n/a
39	MXI1	chr5:154133886-154137235	GM12878	blood:	n/a	n/a
40	SIN3A	chr5:154133973-154138883	H1-hESC	embryonic stem cell:	n/a	chr5:154136477-154136488 chr5:154134277-154134290
41	POLR2A	chr5:154133868-154137145	K562	blood:	n/a	n/a
42	POLR2A	chr5:154134101-154137056	MCF-7	breast:	n/a	n/a
43	TCF7L2	chr5:154134029-154136089	HCT-116	colon:	n/a	n/a
44	CEBPB	chr5:154135773-154136171	Hela-S3	cervix:	n/a	n/a
45	MAX	chr5:154135752-154136981	K562	blood:	n/a	chr5:154136511-154136521 chr5:154136963-154136973 chr5:154136730-154136740
46	POLR2A	chr5:154135581-154137089	H1-hESC	embryonic stem cell:	n/a	n/a
47	MYC	chr5:154133383-154137123	K562	blood:	n/a	chr5:154136511-154136521 chr5:154134523-154134532 chr5:154134538-154134548 chr5:154134657-154134668 chr5:154134656-154134669 chr5:154133516-154133527 chr5:154136963-154136973 chr5:154134650-154134659 chr5:154136730-154136740 chr5:154133517-154133526 chr5:154133518-154133525 chr5:154134657-154134668 chr5:154134658-154134667
48	POLR2A	chr5:154133080-154137254	K562	blood:	n/a	n/a
49	TAF1	chr5:154135605-154136102	K562	blood:	n/a	n/a
50	MYC	chr5:154133238-154137250	K562	blood:	n/a	chr5:154136511-154136521 chr5:154134523-154134532 chr5:154134538-154134548 chr5:154134657-154134668 chr5:154134656-154134669 chr5:154133516-154133527 chr5:154136963-154136973 chr5:154134650-154134659 chr5:154136730-154136740 chr5:154133517-154133526 chr5:154133518-154133525 chr5:154134657-154134668 chr5:154134658-154134667

No.	Distal block	Cell Line	Cell type
1	chr5:154135101..154137187-chr5:154183739..154185409,2	MCF-7	breast:
2	chr5:154059571..154067369-chr5:154132796..154138140,13	K562	blood:
3	chr5:154091014..154094062-chr5:154133007..154138054,7	MCF-7	breast:
4	chr5:154090008..154095548-chr5:154132332..154137735,10	MCF-7	breast:
5	chr5:154133833..154138436-chr5:154316104..154319386,7	K562	blood:
6	chr5:154133318..154137368-chr5:154208082..154212477,8	MCF-7	breast:
7	chr5:154059219..154066449-chr5:154131053..154139153,28	MCF-7	breast:
8	chr5:154092401..154094147-chr5:154134615..154136737,2	K562	blood:
9	chr5:154079413..154083903-chr5:154131964..154138437,9	MCF-7	breast:
10	chr5:154133224..154141155-chr5:154235246..154242227,24	MCF-7	breast:
11	chr17:59475759..59478103-chr5:154134019..154136422,2	MCF-7	breast:
12	chr5:154133665..154137234-chr5:154235811..154241105,6	MCF-7	breast:
13	chr5:154133563..154137747-chr5:154235219..154239187,9	K562	blood:
14	chr5:154134478..154136259-chr5:156568877..156571318,2	K562	blood:
15	chr5:154133598..154138734-chr5:154235660..154239806,12	K562	blood:
16	chr5:154133984..154137613-chr5:154316996..154320177,4	K562	blood:
17	chr5:154134637..154137206-chr5:154228501..154230611,2	MCF-7	breast:
18	chr5:154134899..154136801-chr5:154190010..154191609,2	K562	blood:

Variant related genes	Relation type
LARP1	TF binding region
ENSG00000121068	Chromatin interaction
ENSG00000155506	Chromatin interaction
ENSG00000155868	Chromatin interaction
ENSG00000155508	Chromatin interaction
ENSG00000135077	Chromatin interaction
ENSG00000221552	Chromatin interaction
ENSG00000263478	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000113263	Chromatin interaction
ENSG00000082516	Chromatin interaction
ENSG00000263361	Chromatin interaction
ENSG00000170271	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1035368	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs11167705	0.91[ASN][1000 genomes]
rs12187921	0.85[CHB][hapmap]
rs12188828	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12300	0.86[JPT][hapmap]
rs1233078	1.00[ASW][hapmap];0.91[CEU][hapmap];0.97[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs158134	0.83[ASN][1000 genomes]
rs17116411	0.83[ASN][1000 genomes]
rs17116414	0.83[ASN][1000 genomes]
rs17116421	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17116433	0.85[CHB][hapmap]
rs17116442	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17116534	0.86[JPT][hapmap]
rs1974776	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs1974777	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs2042168	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2112223	0.86[JPT][hapmap]
rs2161128	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2258437	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2544860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2544875	0.82[ASN][1000 genomes]
rs2544880	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2544884	0.85[CHD][hapmap]
rs255529	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2644743	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs2644744	0.86[JPT][hapmap]
rs2688186	0.82[ASN][1000 genomes]
rs2688188	0.82[ASN][1000 genomes]
rs2688191	0.82[ASN][1000 genomes]
rs2688193	0.82[ASN][1000 genomes]
rs2688198	0.86[JPT][hapmap]
rs2688200	0.81[ASN][1000 genomes]
rs2688201	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2688208	0.86[JPT][hapmap]
rs286624	0.83[ASN][1000 genomes]
rs32427	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs348739	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs348749	0.82[CHB][hapmap]
rs348750	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs348752	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs39614	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4623203	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs56374414	0.86[ASN][1000 genomes]
rs58415346	0.86[ASN][1000 genomes]
rs59525998	0.86[ASN][1000 genomes]
rs6580122	0.90[ASN][1000 genomes]
rs6873483	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6876004	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6884416	0.82[ASN][1000 genomes]
rs702742	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs73276742	0.86[ASN][1000 genomes]
rs7723269	0.83[ASN][1000 genomes]
rs816717	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs816718	0.82[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs816720	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs816734	0.95[ASN][1000 genomes]
rs816747	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021153	chr5:154099869-154147970	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	esv3406300	chr5:154133209-154138557	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
3	esv3442367	chr5:154133259-154137657	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
4	esv3371359	chr5:154133784-154136632	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs960499	LARP1	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154133400-154137200	Active TSS	Lung	lung
2	chr5:154133600-154137600	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr5:154133800-154137200	Active TSS	Esophagus	oesophagus
4	chr5:154133800-154137600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:154133800-154137600	Active TSS	Psoas Muscle	Psoas
6	chr5:154134000-154137600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:154134000-154137600	Active TSS	H9 Cell Line	embryonic stem cell
8	chr5:154134000-154137600	Active TSS	Aorta	Aorta
9	chr5:154134000-154137600	Active TSS	Brain Anterior Caudate	brain
10	chr5:154134000-154137600	Active TSS	Brain Substantia Nigra	brain
11	chr5:154134000-154137600	Active TSS	Fetal Brain Female	brain
12	chr5:154134000-154137600	Active TSS	Fetal Kidney	kidney
13	chr5:154134000-154137600	Active TSS	Rectal Mucosa Donor 31	rectum
14	chr5:154134000-154137800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr5:154134000-154137800	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr5:154134000-154137800	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr5:154134000-154138200	Active TSS	Ovary	ovary
18	chr5:154134000-154138400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr5:154134000-154138600	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr5:154134200-154137000	Active TSS	Sigmoid Colon	Sigmoid Colon
21	chr5:154134200-154137000	Active TSS	Spleen	Spleen
22	chr5:154134200-154137200	Active TSS	Gastric	stomach
23	chr5:154134200-154137600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr5:154134200-154137600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr5:154134200-154137600	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr5:154134200-154137600	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr5:154134200-154137600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr5:154134200-154137600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr5:154134200-154137600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr5:154134200-154137600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr5:154134200-154137600	Active TSS	Brain Cingulate Gyrus	brain
32	chr5:154134200-154137600	Active TSS	Brain Hippocampus Middle	brain
33	chr5:154134200-154137600	Active TSS	Brain Inferior Temporal Lobe	brain
34	chr5:154134200-154137600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr5:154134200-154137600	Active TSS	Colon Smooth Muscle	Colon
36	chr5:154134200-154137600	Active TSS	Fetal Lung	lung
37	chr5:154134200-154137600	Active TSS	Fetal Stomach	stomach
38	chr5:154134200-154137600	Active TSS	Small Intestine	intestine
39	chr5:154134200-154137600	Active TSS	A549	lung
40	chr5:154134200-154137600	Active TSS	Hela-S3	cervix
41	chr5:154134200-154137800	Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr5:154134200-154137800	Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr5:154134200-154137800	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr5:154134400-154137000	Active TSS	Primary B cells from peripheral blood	blood
45	chr5:154134400-154137000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr5:154134400-154137200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr5:154134400-154137200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr5:154134400-154137200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
49	chr5:154134400-154137200	Active TSS	Left Ventricle	heart
50	chr5:154134400-154137200	Active TSS	Placenta Amnion	Placenta Amnion

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