Variant report

Variant	rs6151599
Chromosome Location	chr5:79951032-79951033
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	chr5:79949416-79951701	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr5:79949816-79951683	Raji	blood:	n/a	n/a
3	MAX	chr5:79950519-79951352	A549	lung:	n/a	n/a
4	POLR2A	chr5:79950825-79951110	HepG2	liver:	n/a	n/a
5	EGR1	chr5:79950590-79951054	K562	blood:	n/a	chr5:79950819-79950832 chr5:79950824-79950834 chr5:79950823-79950833 chr5:79950847-79950860 chr5:79950819-79950832 chr5:79950818-79950833
6	GTF2F1	chr5:79950492-79951092	K562	blood:	n/a	n/a
7	ETS1	chr5:79950477-79951173	GM12878	blood:	n/a	chr5:79950479-79950492 chr5:79950822-79950833
8	RCOR1	chr5:79950468-79951088	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr5:79949826-79951549	GM19193	blood:	n/a	n/a
10	POLR2A	chr5:79949921-79951367	GM10847	blood:	n/a	n/a
11	POLR2A	chr5:79950193-79951246	MCF10A-Er-Src	breast:	n/a	n/a
12	ZMIZ1	chr5:79950469-79951492	K562	blood:	n/a	n/a
13	JUND	chr5:79950503-79951091	H1-hESC	embryonic stem cell:	n/a	chr5:79950822-79950831 chr5:79950823-79950832
14	TAF1	chr5:79950861-79951109	Hela-S3	cervix:	n/a	n/a
15	PML	chr5:79950824-79951256	K562	blood:	n/a	n/a
16	SIN3A	chr5:79949104-79951221	H1-hESC	embryonic stem cell:	n/a	chr5:79950816-79950827 chr5:79949531-79949539
17	POLR2A	chr5:79950402-79951134	ECC-1	luminal epithelium:	n/a	n/a
18	POLR2A	chr5:79949794-79951638	MCF-7	breast:	n/a	n/a
19	ELK1	chr5:79950490-79951206	GM12878	blood:	n/a	n/a
20	YY1	chr5:79950817-79951133	GM12891	blood:	n/a	chr5:79950849-79950858 chr5:79950824-79950833
21	POLR2A	chr5:79949851-79951173	H1-hESC	embryonic stem cell:	n/a	n/a
22	CHD2	chr5:79950503-79951071	H1-hESC	embryonic stem cell:	n/a	n/a
23	STAT5A	chr5:79950433-79951300	GM12878	blood:	n/a	n/a
24	POLR2A	chr5:79949856-79951727	GM19099	blood:	n/a	n/a
25	GTF2B	chr5:79950882-79951158	K562	blood:	n/a	n/a
26	RELA	chr5:79950458-79951397	GM15510	blood:	n/a	n/a
27	POLR2A	chr5:79950231-79951331	HUVEC	blood vessel:	n/a	n/a
28	WRNIP1	chr5:79950538-79951574	GM12878	blood:	n/a	n/a
29	TAF1	chr5:79949869-79951146	H1-hESC	embryonic stem cell:	n/a	n/a
30	ELF1	chr5:79950773-79951299	A549	lung:	n/a	chr5:79950849-79950858
31	SIN3AK20	chr5:79949748-79951402	MCF-7	breast:	n/a	n/a
32	RFX5	chr5:79950841-79951152	GM12878	blood:	n/a	n/a
33	POLR2A	chr5:79948603-79951714	GM12878	blood:	n/a	n/a
34	YY1	chr5:79950361-79951319	GM12878	blood:	n/a	chr5:79950849-79950858 chr5:79950385-79950394 chr5:79950824-79950833 chr5:79950816-79950827 chr5:79950380-79950394 chr5:79950805-79950824
35	SP1	chr5:79950491-79951178	H1-hESC	embryonic stem cell:	n/a	chr5:79950825-79950834 chr5:79950851-79950862 chr5:79950820-79950834 chr5:79950853-79950862 chr5:79950824-79950834 chr5:79950824-79950833 chr5:79950823-79950834 chr5:79950895-79950904 chr5:79950823-79950835 chr5:79950825-79950834 chr5:79950852-79950861 chr5:79950824-79950834 chr5:79950823-79950835
36	TAF1	chr5:79950438-79951322	ECC-1	luminal epithelium:	n/a	n/a
37	TAF1	chr5:79950403-79951182	MCF-7	breast:	n/a	n/a
38	POLR2A	chr5:79950030-79951245	GM12892	blood:	n/a	n/a
39	POLR2A	chr5:79949736-79951618	GM12878	blood:	n/a	n/a
40	TEAD4	chr5:79950425-79951117	K562	blood:	n/a	n/a
41	PML	chr5:79950402-79951202	MCF-7	breast:	n/a	n/a
42	MAX	chr5:79950040-79951252	HCT-116	colon:	n/a	n/a
43	MAZ	chr5:79950500-79951071	HepG2	liver:	n/a	n/a
44	SPI1	chr5:79950812-79951184	HL-60	blood:	n/a	n/a
45	TAF7	chr5:79950336-79951147	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr5:79950079-79951231	HCT-116	colon:	n/a	n/a
47	GABPA	chr5:79950476-79951411	MCF-7	breast:	n/a	chr5:79950824-79950833 chr5:79950846-79950855
48	MBD4	chr5:79950822-79951265	HepG2	liver:	n/a	n/a
49	CCNT2	chr5:79949448-79951322	K562	blood:	n/a	chr5:79950385-79950394 chr5:79950824-79950833 chr5:79950816-79950825
50	E2F4	chr5:79949922-79951078	K562	blood:	n/a	chr5:79950363-79950371 chr5:79950516-79950526 chr5:79950368-79950375 chr5:79950852-79950861 chr5:79950367-79950376 chr5:79950368-79950375 chr5:79950824-79950833 chr5:79950368-79950375 chr5:79950385-79950394

No.	Distal block	Cell Line	Cell type
1	chr5:79950548..79951545-chr7:5569740..5570286,2	Hela-S3	cervix:
2	chr11:85955785..85956525-chr5:79950777..79951467,2	NB4	blood:
3	chr5:79950108..79951095-chr6:27860383..27860953,2	Hela-S3	cervix:
4	chr5:79781713..79786255-chr5:79948613..79954295,12	MCF-7	breast:
5	chr5:79782822..79786705-chr5:79948261..79952248,11	MCF-7	breast:
6	chr5:79918045..79920951-chr5:79949482..79951097,2	MCF-7	breast:
7	chr5:79950349..79951063-chrX:23685473..23686093,2	Hela-S3	cervix:
8	chr5:79702114..79706204-chr5:79947823..79953616,8	MCF-7	breast:
9	chr12:105379925..105380593-chr5:79950231..79951164,2	HCT-116	colon:
10	chr5:79950686..79951228-chr6:105850772..105851601,2	NB4	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM151B-3	chr5:79950971-79951398	NONHSAT102418

Variant related genes	Relation type
MTRNR2L2	TF binding region
DHFR	TF binding region
ENSG00000074266	Chromatin interaction
ENSG00000151131	Chromatin interaction
ENSG00000152380	Chromatin interaction
ENSG00000249042	Chromatin interaction
ENSG00000039319	Chromatin interaction
ENSG00000123131	Chromatin interaction
ENSG00000085377	Chromatin interaction
ENSG00000075624	Chromatin interaction
ENSG00000251221	Chromatin interaction
ENSG00000197153	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10036264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10052238	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10054574	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10057770	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10072026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10077031	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10078190	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10213944	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10474631	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10474632	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs10474634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11741448	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11742668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11742720	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11749051	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13355622	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56270084	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6151606	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6151640	1.00[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs6151655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6453522	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67695365	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72765574	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72765575	0.90[EUR][1000 genomes];1.00[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	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3406922	chr5:79949421-79951969	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79948600-79951200	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr5:79948600-79952000	Active TSS	GM12878-XiMat	blood
3	chr5:79948800-79951400	Active TSS	Fetal Intestine Large	intestine
4	chr5:79949000-79951200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr5:79949000-79951200	Active TSS	Stomach Mucosa	stomach
6	chr5:79949000-79951400	Active TSS	H1 Cell Line	embryonic stem cell
7	chr5:79949000-79951400	Active TSS	H9 Cell Line	embryonic stem cell
8	chr5:79949000-79951400	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr5:79949000-79951400	Active TSS	Fetal Intestine Small	intestine
10	chr5:79949000-79951600	Active TSS	A549	lung
11	chr5:79949200-79951200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:79949200-79951200	Active TSS	Brain Cingulate Gyrus	brain
13	chr5:79949200-79951400	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr5:79949200-79951400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr5:79949200-79951400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr5:79949200-79951600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr5:79949200-79951600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr5:79949200-79951600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr5:79949200-79951600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr5:79949200-79952000	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr5:79949400-79951400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:79949400-79951400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr5:79949400-79951400	Active TSS	NHLF	lung
24	chr5:79949400-79951600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr5:79949600-79951200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr5:79949600-79951200	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr5:79949600-79951200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr5:79949600-79951200	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr5:79949600-79951200	Active TSS	Hela-S3	cervix
30	chr5:79949600-79951200	Active TSS	NHDF-Ad	bronchial
31	chr5:79949600-79951400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr5:79949600-79951400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr5:79949600-79951400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr5:79949600-79951400	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr5:79949600-79951400	Active TSS	HepG2	liver
36	chr5:79949600-79951400	Active TSS	HMEC	breast
37	chr5:79949600-79951400	Active TSS	HSMMtube	muscle
38	chr5:79949600-79952000	Active TSS	K562	blood
39	chr5:79949800-79951200	Active TSS	Primary hematopoietic stem cells short term culture	blood
40	chr5:79949800-79951200	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr5:79949800-79951200	Active TSS	NHEK	skin
42	chr5:79949800-79951400	Active TSS	Muscle Satellite Cultured Cells	--
43	chr5:79949800-79951400	Active TSS	Fetal Kidney	kidney
44	chr5:79949800-79951400	Active TSS	HSMM	muscle
45	chr5:79950000-79951200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr5:79950000-79951200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr5:79950000-79951200	Active TSS	Brain Angular Gyrus	brain
48	chr5:79950000-79951200	Active TSS	Brain Anterior Caudate	brain
49	chr5:79950000-79951200	Active TSS	Fetal Brain Male	brain
50	chr5:79950000-79951200	Active TSS	Fetal Lung	lung

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