Variant report

Variant	rs965235
Chromosome Location	chr5:154063295-154063296
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	MAX	chr5:154061928-154063395	A549	lung:	n/a	chr5:154062543-154062552 chr5:154062180-154062189 chr5:154062180-154062191
2	RAD21	chr5:154061517-154063318	SK-N-SH	brain:	n/a	chr5:154062312-154062325 chr5:154062672-154062684 chr5:154062061-154062074
3	JUND	chr5:154061987-154063373	Hela-S3	cervix:	n/a	chr5:154062543-154062553 chr5:154062542-154062554 chr5:154062545-154062552 chr5:154062544-154062552 chr5:154062544-154062552 chr5:154062542-154062553
4	MXI1	chr5:154061415-154063637	SK-N-SH	brain:	n/a	chr5:154062180-154062189
5	SMARCC1	chr5:154062046-154063562	Hela-S3	cervix:	n/a	chr5:154062544-154062553
6	JUND	chr5:154061860-154063413	SK-N-SH	brain:	n/a	chr5:154062543-154062553 chr5:154062542-154062554 chr5:154062545-154062552 chr5:154062544-154062552 chr5:154062544-154062552 chr5:154062542-154062553
7	FOS	chr5:154062048-154063483	MCF10A-Er-Src	breast:	n/a	chr5:154062543-154062553 chr5:154062542-154062554 chr5:154062545-154062552 chr5:154062544-154062552 chr5:154062542-154062553 chr5:154062544-154062552
8	CTCF	chr5:154061710-154063446	SK-N-SH	brain:	n/a	chr5:154062319-154062332 chr5:154062069-154062082
9	POLR2A	chr5:154062050-154063588	MCF10A-Er-Src	breast:	n/a	n/a
10	JUN	chr5:154061777-154063927	K562	blood:	n/a	chr5:154062543-154062553 chr5:154062542-154062554 chr5:154062545-154062552 chr5:154062544-154062552 chr5:154062544-154062552
11	TCF12	chr5:154061739-154063424	A549	lung:	n/a	n/a
12	POLR2A	chr5:154062940-154063427	SK-N-MC	brain:	n/a	n/a
13	USF2	chr5:154063175-154063415	Hela-S3	cervix:	n/a	chr5:154063260-154063271
14	MAZ	chr5:154061947-154063339	Hela-S3	cervix:	n/a	chr5:154062543-154062552 chr5:154062180-154062189 chr5:154062180-154062191
15	POLR2A	chr5:154063154-154063436	HepG2	liver:	n/a	n/a
16	GTF2F1	chr5:154062905-154063391	Hela-S3	cervix:	n/a	n/a
17	ZNF263	chr5:154061972-154063304	HEK293-T-REx	kidney:	n/a	chr5:154062501-154062522 chr5:154062456-154062477 chr5:154062320-154062329 chr5:154062434-154062455
18	POLR2A	chr5:154063206-154063355	MCF10A-Er-Src	breast:	n/a	n/a
19	MAX	chr5:154061933-154063340	Hela-S3	cervix:	n/a	chr5:154062543-154062552 chr5:154062180-154062189 chr5:154062180-154062191
20	FOS	chr5:154062044-154063837	MCF10A-Er-Src	breast:	n/a	chr5:154062543-154062553 chr5:154062542-154062554 chr5:154062545-154062552 chr5:154062544-154062552 chr5:154062542-154062553 chr5:154062544-154062552
21	MXI1	chr5:154061922-154063672	IMR90	lung:	n/a	chr5:154062180-154062189
22	MAZ	chr5:154061942-154063501	IMR90	lung:	n/a	chr5:154062543-154062552 chr5:154062180-154062189 chr5:154062180-154062191
23	MAX	chr5:154061944-154063457	HCT-116	colon:	n/a	chr5:154062543-154062552 chr5:154062180-154062189 chr5:154062180-154062191
24	REST	chr5:154061931-154063348	A549	lung:	n/a	chr5:154062328-154062338 chr5:154062563-154062581
25	POLR2A	chr5:154063160-154063783	PANC-1	pancreas:	n/a	n/a
26	MAX	chr5:154061940-154063358	HCT-116	colon:	n/a	chr5:154062543-154062552 chr5:154062180-154062189 chr5:154062180-154062191
27	MAX	chr5:154061938-154063331	HepG2	liver:	n/a	chr5:154062543-154062552 chr5:154062180-154062189 chr5:154062180-154062191
28	JUND	chr5:154061901-154063325	K562	blood:	n/a	chr5:154062543-154062553 chr5:154062542-154062554 chr5:154062545-154062552 chr5:154062544-154062552 chr5:154062544-154062552 chr5:154062542-154062553

No.	Distal block	Cell Line	Cell type
1	chr5:154059219..154066449-chr5:154131053..154139153,28	MCF-7	breast:
2	chr5:154032924..154035953-chr5:154060890..154064401,4	K562	blood:
3	chr5:154061087..154064928-chr5:154133720..154137511,10	MCF-7	breast:
4	chr5:154062083..154065077-chr5:154078214..154080372,2	K562	blood:
5	chr5:154053688..154055424-chr5:154062643..154064722,2	K562	blood:
6	chr5:154061692..154063624-chr5:154081496..154083811,3	MCF-7	breast:
7	chr5:154057419..154059228-chr5:154060984..154063481,2	MCF-7	breast:
8	chr5:154062466..154064358-chr5:154453743..154456113,2	K562	blood:
9	chr5:154062284..154064360-chr5:154130861..154133550,2	MCF-7	breast:
10	chr5:154061423..154063859-chr5:154072276..154076586,3	K562	blood:
11	chr5:154059571..154067369-chr5:154132796..154138140,13	K562	blood:
12	chr5:154061441..154064069-chr5:154090774..154094018,3	MCF-7	breast:
13	chr5:154061792..154064615-chr5:154236472..154239583,3	MCF-7	breast:
14	chr5:154062816..154065132-chr5:154065984..154069776,3	MCF-7	breast:
15	chr5:154060599..154064575-chr5:154133211..154138140,11	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LARP1-2	chr5:154062216-154065204	NONHSAT104706

Variant related genes	Relation type
MIR1303	TF binding region
ENSG00000155508	Chromatin interaction
ENSG00000263478	Chromatin interaction
ENSG00000155506	Chromatin interaction
ENSG00000170271	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10039709	1.00[CEU][hapmap];0.87[GIH][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs10074675	0.82[EUR][1000 genomes]
rs10875591	0.81[AMR][1000 genomes]
rs12652072	0.84[ASW][hapmap]
rs1862130	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1862131	0.88[EUR][1000 genomes]
rs1972618	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2052448	0.82[EUR][1000 genomes]
rs2396995	0.80[AMR][1000 genomes]
rs3893695	0.82[EUR][1000 genomes]
rs4117784	0.81[GIH][hapmap]
rs4958382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958384	0.82[EUR][1000 genomes]
rs4958385	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs4958387	0.82[EUR][1000 genomes]
rs4958758	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4958759	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4958760	0.88[EUR][1000 genomes]
rs4958761	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4958762	0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs4958765	0.83[GIH][hapmap]
rs6580099	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6580101	0.80[EUR][1000 genomes]
rs6580102	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6580103	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs6580104	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6580107	0.82[EUR][1000 genomes]
rs6580108	0.83[AMR][1000 genomes]
rs6580109	0.82[AMR][1000 genomes]
rs6580111	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6868098	1.00[CEU][hapmap];0.87[GIH][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes]
rs749777	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.80[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7715775	0.82[EUR][1000 genomes]
rs7721183	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7736062	0.82[EUR][1000 genomes]
rs918365	0.80[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9324791	1.00[CEU][hapmap];0.87[CHB][hapmap];0.84[EUR][1000 genomes]
rs9324792	1.00[CEU][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.83[TSI][hapmap];0.84[EUR][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	nsv462491	chr5:154045280-154066205	Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv600090	chr5:154045280-154066205	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154060800-154070000	Weak transcription	Gastric	stomach
2	chr5:154061600-154063400	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr5:154061600-154063400	Active TSS	Brain Cingulate Gyrus	brain
4	chr5:154061600-154063600	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr5:154061600-154063800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:154061800-154063400	Active TSS	Brain Hippocampus Middle	brain
7	chr5:154061800-154063400	Active TSS	Fetal Kidney	kidney
8	chr5:154062000-154063400	Active TSS	H9 Cell Line	embryonic stem cell
9	chr5:154062000-154063400	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr5:154062000-154063400	Flanking Active TSS	Dnd41	blood
11	chr5:154062000-154063600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:154062200-154063600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:154062600-154063400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr5:154062600-154063400	Flanking Active TSS	Hela-S3	cervix
15	chr5:154062600-154063400	Flanking Active TSS	HepG2	liver
16	chr5:154062600-154063600	Flanking Active TSS	Liver	Liver
17	chr5:154062600-154063600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr5:154062600-154063600	Flanking Active TSS	K562	blood
19	chr5:154062600-154063600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr5:154062600-154063800	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr5:154062800-154063400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr5:154062800-154063400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
23	chr5:154062800-154063400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr5:154062800-154063400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr5:154062800-154063400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
26	chr5:154062800-154063400	Flanking Active TSS	Rectal Smooth Muscle	rectum
27	chr5:154062800-154063400	Enhancers	Small Intestine	intestine
28	chr5:154062800-154063400	Flanking Active TSS	GM12878-XiMat	blood
29	chr5:154062800-154063600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr5:154062800-154063600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr5:154062800-154063600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr5:154062800-154063600	Flanking Active TSS	Colon Smooth Muscle	Colon
33	chr5:154062800-154063600	Flanking Active TSS	Duodenum Mucosa	Duodenum
34	chr5:154062800-154064600	Enhancers	Esophagus	oesophagus
35	chr5:154063000-154063400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr5:154063000-154063400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr5:154063000-154063400	Enhancers	Primary B cells from peripheral blood	blood
38	chr5:154063000-154063400	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr5:154063000-154063400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr5:154063000-154063400	Flanking Active TSS	Brain Angular Gyrus	brain
41	chr5:154063000-154063400	Enhancers	Brain Anterior Caudate	brain
42	chr5:154063000-154063400	Active TSS	Fetal Brain Male	brain
43	chr5:154063000-154063400	Flanking Active TSS	Psoas Muscle	Psoas
44	chr5:154063000-154063400	Flanking Active TSS	Right Atrium	heart
45	chr5:154063000-154063400	Flanking Active TSS	A549	lung
46	chr5:154063000-154063600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr5:154063000-154063600	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr5:154063000-154063600	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr5:154063000-154063600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr5:154063000-154063600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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