Variant report

Variant	rs3806940
Chromosome Location	chr5:96270725-96270726
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	chr5:96270016-96272242	MCF-7	breast:	n/a	n/a
2	CTCF	chr5:96270720-96270870	GM06990	blood:	n/a	n/a
3	GATA2	chr5:96270418-96271389	HUVEC	blood vessel:	n/a	chr5:96271207-96271221
4	BHLHE40	chr5:96269756-96271951	K562	blood:	n/a	chr5:96271596-96271612
5	HDAC2	chr5:96270217-96272000	MCF-7	breast:	n/a	n/a
6	SP1	chr5:96270182-96272124	HCT-116	colon:	n/a	chr5:96271598-96271607 chr5:96271597-96271607 chr5:96271596-96271608 chr5:96271597-96271607 chr5:96271597-96271606 chr5:96271596-96271608 chr5:96271597-96271606 chr5:96271597-96271611
7	POLR2A	chr5:96269126-96273104	GM12892	blood:	n/a	n/a
8	POLR2A	chr5:96268968-96273188	GM12878	blood:	n/a	n/a
9	MYBL2	chr5:96270177-96271983	HepG2	liver:	n/a	n/a
10	FOXA1	chr5:96270110-96271231	HepG2	liver:	n/a	n/a
11	TBL1XR1	chr5:96269576-96271956	GM12878	blood:	n/a	n/a
12	CHD1	chr5:96267264-96273025	GM12878	blood:	n/a	n/a
13	HEY1	chr5:96270061-96271938	HepG2	liver:	n/a	chr5:96271533-96271548
14	ZBTB7A	chr5:96270645-96271141	HepG2	liver:	n/a	n/a
15	POLR2A	chr5:96269471-96272024	PBDE	blood:	n/a	n/a
16	CTCF	chr5:96270700-96270850	AG04450	lung:	n/a	n/a
17	MAX	chr5:96269837-96272170	A549	lung:	n/a	n/a
18	BHLHE40	chr5:96270318-96271197	HepG2	liver:	n/a	n/a
19	GATA2	chr5:96269955-96271901	SH-SY5Y	brain:	n/a	chr5:96271207-96271221
20	TCF12	chr5:96270080-96272068	ECC-1	luminal epithelium:	n/a	chr5:96271640-96271650
21	TAF1	chr5:96269950-96271306	K562	blood:	n/a	n/a
22	POLR2A	chr5:96270237-96272074	PFSK-1	brain:	n/a	n/a
23	SP1	chr5:96270438-96272009	GM12878	blood:	n/a	chr5:96271598-96271607 chr5:96271597-96271607 chr5:96271596-96271608 chr5:96271597-96271607 chr5:96271597-96271606 chr5:96271596-96271608 chr5:96271597-96271606 chr5:96271597-96271611
24	MAX	chr5:96269837-96272676	A549	lung:	n/a	n/a
25	POLR2A	chr5:96269090-96273351	GM12878	blood:	n/a	n/a
26	RAD21	chr5:96270213-96272288	IMR90	lung:	n/a	chr5:96271600-96271610
27	BCL3	chr5:96270350-96271310	GM12878	blood:	n/a	n/a
28	TCF12	chr5:96270687-96271278	A549	lung:	n/a	n/a
29	EBF1	chr5:96270232-96271430	GM12878	blood:	n/a	n/a
30	NR3C1	chr5:96270662-96271258	A549	lung:	n/a	n/a
31	USF1	chr5:96270386-96271225	SK-N-SH	brain:	n/a	n/a
32	ELF1	chr5:96270458-96271241	SK-N-SH	brain:	n/a	n/a
33	SP1	chr5:96270647-96271970	H1-hESC	embryonic stem cell:	n/a	chr5:96271598-96271607 chr5:96271597-96271607 chr5:96271596-96271608 chr5:96271597-96271607 chr5:96271597-96271606 chr5:96271596-96271608 chr5:96271597-96271606 chr5:96271597-96271611
34	TAF1	chr5:96270229-96271254	GM12891	blood:	n/a	n/a
35	FOXA1	chr5:96270228-96271098	HepG2	liver:	n/a	n/a
36	YY1	chr5:96269960-96271121	HepG2	liver:	n/a	n/a
37	SIN3AK20	chr5:96270392-96271068	PFSK-1	brain:	n/a	n/a
38	TRIM28	chr5:96270390-96271243	K562	blood:	n/a	n/a
39	POLR2A	chr5:96269916-96272567	MCF10A-Er-Src	breast:	n/a	n/a
40	FOXA1	chr5:96270176-96271095	HepG2	liver:	n/a	n/a
41	BCL11A	chr5:96270684-96271090	GM12878	blood:	n/a	n/a
42	JUND	chr5:96270315-96272052	A549	lung:	n/a	n/a
43	STAT3	chr5:96270503-96271090	MCF10A-Er-Src	breast:	n/a	n/a
44	POLR2A	chr5:96270074-96271999	HepG2	liver:	n/a	n/a
45	CTCF	chr5:96270469-96271268	GM12878	blood:	n/a	n/a
46	POLR2A	chr5:96270258-96272015	K562	blood:	n/a	n/a
47	CTCF	chr5:96270680-96270830	GM12874	blood:	n/a	n/a
48	CTCF	chr5:96270700-96270850	K562	blood:	n/a	n/a
49	MEF2C	chr5:96270233-96271239	GM12878	blood:	n/a	n/a
50	MAX	chr5:96270008-96272708	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:96093022..96094716-chr5:96270503..96272835,2	MCF-7	breast:
2	chr5:96267069..96273023-chr5:96293959..96302488,9	K562	blood:
3	chr5:96140726..96144602-chr5:96269258..96273227,6	MCF-7	breast:
4	chr5:96269896..96271438-chr5:96517931..96519494,2	MCF-7	breast:
5	chr5:95997114..95998690-chr5:96269799..96271534,2	MCF-7	breast:
6	chr5:96270050..96274625-chr5:96293478..96297387,4	MCF-7	breast:
7	chr5:96269264..96270961-chr5:96303630..96305145,2	MCF-7	breast:
8	chr12:53294589..53297391-chr5:96270042..96272818,2	MCF-7	breast:
9	chr5:96270371..96272445-chr8:126010140..126012494,2	MCF-7	breast:
10	chr5:96210744..96214555-chr5:96268958..96271606,4	MCF-7	breast:
11	chr5:96140146..96144558-chr5:96269495..96273172,12	MCF-7	breast:
12	chr5:96268234..96272758-chr5:96290815..96294670,4	K562	blood:
13	chr5:96270007..96273203-chr5:96295277..96299165,4	K562	blood:
14	chr1:144533657..144534237-chr5:96270556..96271167,2	Hela-S3	cervix:
15	chr5:96087767..96089736-chr5:96268436..96270992,2	MCF-7	breast:
16	chr19:13263910..13264612-chr5:96270303..96271295,2	Hela-S3	cervix:
17	chr5:96268127..96270774-chr5:96299213..96300719,2	K562	blood:
18	chr5:96207193..96215079-chr5:96269183..96273335,11	MCF-7	breast:
19	chr11:82996621..82997375-chr5:96270593..96271497,2	Hela-S3	cervix:
20	chr5:96142546..96145890-chr5:96269908..96273049,5	K562	blood:
21	chr5:96143640..96144362-chr5:96270389..96271299,2	MCF-7	breast:
22	chr5:96141925..96145850-chr5:96265867..96272606,9	K562	blood:
23	chr5:96268650..96270760-chr5:96289002..96291090,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTD-2260A17.2.1-1	chr5:96269826-96271513	NONHSAT102912

Variant related genes	Relation type
LNPEP	TF binding region
ENSG00000164308	Chromatin interaction
ENSG00000113441	Chromatin interaction
ENSG00000267598	Chromatin interaction
ENSG00000272109	Chromatin interaction
ENSG00000255234	Chromatin interaction
ENSG00000137500	Chromatin interaction
ENSG00000153113	Chromatin interaction
ENSG00000251513	Chromatin interaction
ENSG00000058729	Chromatin interaction
ENSG00000253513	Chromatin interaction
ENSG00000247121	Chromatin interaction
ENSG00000170421	Chromatin interaction
ENSG00000104549	Chromatin interaction
ENSG00000201699	Chromatin interaction
ENSG00000200884	Chromatin interaction
ENSG00000164307	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12656253	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12657704	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2287902	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2303210	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3797795	1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3797798	1.00[CHB][hapmap]
rs3797850	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs58477147	1.00[AMR][1000 genomes]
rs58748938	0.80[ASN][1000 genomes]
rs60280354	1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs73141135	0.80[ASN][1000 genomes]
rs73141187	1.00[AMR][1000 genomes]
rs769336	1.00[AMR][1000 genomes]
rs769338	1.00[AMR][1000 genomes]
rs7723473	1.00[AMR][1000 genomes]
rs7728347	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv598962	chr5:96057891-96893164	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv948703	chr5:96078309-96368839	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1027472	chr5:96081592-96337550	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1028741	chr5:96082401-96372165	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv949058	chr5:96082433-96390619	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv598963	chr5:96084776-96363407	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv531967	chr5:96127842-96302702	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 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	chr5:96268200-96274000	Active TSS	GM12878-XiMat	blood
2	chr5:96268400-96271200	Active TSS	Primary T cells fromperipheralblood	blood
3	chr5:96268400-96272600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr5:96268400-96273400	Active TSS	Fetal Thymus	thymus
5	chr5:96268400-96273600	Active TSS	Thymus	Thymus
6	chr5:96269200-96270800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
7	chr5:96269200-96273200	Active TSS	Right Atrium	heart
8	chr5:96269400-96272400	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr5:96269400-96273000	Active TSS	Right Ventricle	heart
10	chr5:96269400-96273600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
11	chr5:96269600-96272600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:96269600-96273000	Active TSS	Brain Angular Gyrus	brain
13	chr5:96269600-96273000	Active TSS	Colonic Mucosa	Colon
14	chr5:96269600-96273800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:96269800-96271600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr5:96269800-96272400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:96269800-96272600	Active TSS	Fetal Brain Female	brain
18	chr5:96269800-96273000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr5:96269800-96273000	Active TSS	Aorta	Aorta
20	chr5:96269800-96273000	Active TSS	Brain Anterior Caudate	brain
21	chr5:96269800-96273000	Active TSS	Fetal Muscle Trunk	muscle
22	chr5:96269800-96273000	Active TSS	Sigmoid Colon	Sigmoid Colon
23	chr5:96269800-96273200	Active TSS	Stomach Smooth Muscle	stomach
24	chr5:96269800-96273600	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr5:96270000-96271800	Bivalent/Poised TSS	HepG2	liver
26	chr5:96270000-96272200	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr5:96270000-96272400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr5:96270000-96272600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr5:96270000-96272600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr5:96270000-96272600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:96270000-96272600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr5:96270000-96272600	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr5:96270000-96272600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
34	chr5:96270000-96272600	Active TSS	Fetal Intestine Large	intestine
35	chr5:96270000-96272600	Active TSS	Rectal Mucosa Donor 29	rectum
36	chr5:96270000-96272600	Active TSS	Dnd41	blood
37	chr5:96270000-96272800	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr5:96270000-96272800	Active TSS	Esophagus	oesophagus
39	chr5:96270000-96272800	Active TSS	Fetal Stomach	stomach
40	chr5:96270000-96272800	Active TSS	Placenta Amnion	Placenta Amnion
41	chr5:96270000-96272800	Active TSS	Small Intestine	intestine
42	chr5:96270000-96272800	Active TSS	A549	lung
43	chr5:96270000-96273000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr5:96270000-96273000	Active TSS	Left Ventricle	heart
45	chr5:96270000-96273000	Active TSS	Lung	lung
46	chr5:96270000-96273000	Active TSS	Ovary	ovary
47	chr5:96270000-96273000	Active TSS	Pancreas	Pancrea
48	chr5:96270000-96273000	Active TSS	Psoas Muscle	Psoas
49	chr5:96270000-96273200	Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr5:96270200-96271000	Active TSS	Primary T regulatory cells fromperipheralblood	blood

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