Variant report

Variant	rs4398764
Chromosome Location	chr6:145119459-145119460
allele	G/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	CBX3	chr6:145118807-145119850	HCT-116	colon:	n/a	n/a
2	SP1	chr6:145118803-145119969	HCT-116	colon:	n/a	n/a
3	TEAD4	chr6:145118952-145119815	HCT-116	colon:	n/a	n/a
4	TEAD4	chr6:145118881-145119773	HCT-116	colon:	n/a	n/a
5	NFIC	chr6:145119116-145119711	SK-N-SH	brain:	n/a	n/a
6	FOS	chr6:145119231-145119576	MCF10A-Er-Src	breast:	n/a	chr6:145119399-145119410
7	TCF12	chr6:145119081-145119853	SK-N-SH	brain:	n/a	chr6:145119381-145119390
8	GATA3	chr6:145119321-145119683	A549	lung:	n/a	n/a
9	EP300	chr6:145119206-145119690	Hela-S3	cervix:	n/a	chr6:145119381-145119391
10	ZBTB33	chr6:145119249-145119594	A549	lung:	n/a	n/a
11	FOS	chr6:145119243-145119654	HUVEC	blood vessel:	n/a	chr6:145119399-145119410
12	SRF	chr6:145118822-145120009	HCT-116	colon:	n/a	n/a
13	JUND	chr6:145119133-145119685	MCF-7	breast:	n/a	n/a
14	RXRA	chr6:145119228-145119714	SK-N-SH	brain:	n/a	n/a
15	GATA3	chr6:145119124-145119818	MCF-7	breast:	n/a	n/a
16	POLR2A	chr6:145119026-145119703	HCT-116	colon:	n/a	n/a
17	POLR2A	chr6:145119076-145119783	PFSK-1	brain:	n/a	n/a
18	GATA3	chr6:145118942-145119863	A549	lung:	n/a	n/a
19	CEBPB	chr6:145118851-145119688	Hela-S3	cervix:	n/a	chr6:145119453-145119464
20	JUND	chr6:145119166-145119737	SK-N-SH	brain:	n/a	n/a
21	FOSL1	chr6:145118911-145119841	HCT-116	colon:	n/a	n/a
22	EP300	chr6:145118978-145119819	A549	lung:	n/a	chr6:145119381-145119391
23	JUND	chr6:145118846-145119976	HCT-116	colon:	n/a	n/a
24	NR2F2	chr6:145119059-145119804	MCF-7	breast:	n/a	n/a
25	NR2F2	chr6:145119112-145119789	MCF-7	breast:	n/a	n/a
26	FOSL2	chr6:145119158-145119714	SK-N-SH	brain:	n/a	n/a
27	JUN	chr6:145118977-145119698	Hela-S3	cervix:	n/a	n/a
28	CEBPB	chr6:145118734-145120030	HCT-116	colon:	n/a	chr6:145119453-145119464
29	MAX	chr6:145119200-145119795	A549	lung:	n/a	n/a
30	STAT3	chr6:145119371-145119642	MCF10A-Er-Src	breast:	n/a	chr6:145119400-145119409 chr6:145119401-145119410
31	RCOR1	chr6:145118943-145119743	Hela-S3	cervix:	n/a	n/a
32	FOS	chr6:145119222-145119695	MCF10A-Er-Src	breast:	n/a	chr6:145119399-145119410
33	TCF12	chr6:145119171-145119728	SK-N-SH	brain:	n/a	chr6:145119381-145119390
34	FOSL2	chr6:145119246-145119650	A549	lung:	n/a	n/a
35	TEAD4	chr6:145119143-145119787	A549	lung:	n/a	n/a
36	EP300	chr6:145119325-145119725	SK-N-SH_RA	brain:	n/a	chr6:145119381-145119391
37	FOSL1	chr6:145118810-145119905	HCT-116	colon:	n/a	n/a
38	EP300	chr6:145119032-145119831	A549	lung:	n/a	chr6:145119381-145119391
39	GATA3	chr6:145119136-145119729	SK-N-SH	brain:	n/a	n/a
40	USF1	chr6:145119292-145119604	A549	lung:	n/a	n/a
41	JUND	chr6:145119147-145119705	SK-N-SH	brain:	n/a	n/a
42	SP1	chr6:145119072-145119769	A549	lung:	n/a	n/a
43	EP300	chr6:145119430-145119782	SK-N-SH_RA	brain:	n/a	n/a
44	JUND	chr6:145118877-145119944	HCT-116	colon:	n/a	n/a
45	JUN	chr6:145119222-145119649	HUVEC	blood vessel:	n/a	n/a
46	FOSL2	chr6:145119129-145119714	MCF-7	breast:	n/a	n/a
47	MAFK	chr6:145118989-145119740	Hela-S3	cervix:	n/a	n/a
48	FOSL2	chr6:145119208-145119614	MCF-7	breast:	n/a	n/a
49	GABPA	chr6:145119220-145119688	A549	lung:	n/a	n/a
50	GATA3	chr6:145119088-145119816	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
UTRN	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs17074240	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17074256	0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17074272	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7762384	1.00[MEX][hapmap]
rs869590	1.00[MEX][hapmap]
rs9497089	0.87[AMR][1000 genomes]
rs9497092	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016747	chr6:144917411-145599874	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv830833	chr6:145001310-145201143	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv886740	chr6:145105354-145199259	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:145046000-145122200	Weak transcription	Colonic Mucosa	Colon
2	chr6:145066200-145126200	Weak transcription	Stomach Mucosa	stomach
3	chr6:145084000-145155800	Weak transcription	Right Ventricle	heart
4	chr6:145085800-145134800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:145089600-145138400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:145090000-145136800	Weak transcription	Fetal Heart	heart
7	chr6:145091000-145145000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:145093400-145119800	Weak transcription	Fetal Intestine Small	intestine
9	chr6:145094400-145136800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr6:145099600-145165800	Weak transcription	Small Intestine	intestine
11	chr6:145100000-145137600	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr6:145100400-145125600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr6:145100400-145133200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr6:145100400-145145000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr6:145102200-145123600	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr6:145107800-145121000	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr6:145108400-145120600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:145110200-145124200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:145110400-145137000	Strong transcription	Primary B cells from cord blood	blood
20	chr6:145110800-145120600	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr6:145113600-145119600	Weak transcription	NHEK	skin
22	chr6:145113600-145126400	Weak transcription	Brain Substantia Nigra	brain
23	chr6:145113800-145120000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr6:145114200-145135600	Strong transcription	Primary B cells from peripheral blood	blood
25	chr6:145114600-145120600	Strong transcription	Duodenum Mucosa	Duodenum
26	chr6:145114600-145120800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:145114600-145121200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr6:145114800-145119800	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr6:145115200-145155000	Weak transcription	Esophagus	oesophagus
30	chr6:145115600-145121400	Strong transcription	Primary T cells from cord blood	blood
31	chr6:145115600-145131400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr6:145115600-145134800	Weak transcription	Lung	lung
33	chr6:145115800-145156600	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr6:145116000-145119600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:145116000-145120000	Weak transcription	Gastric	stomach
36	chr6:145116000-145120600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr6:145116000-145125600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr6:145116000-145142000	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr6:145116000-145148600	Weak transcription	Placenta	Placenta
40	chr6:145116000-145154800	Weak transcription	Spleen	Spleen
41	chr6:145116000-145155800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr6:145116200-145125600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr6:145116200-145154400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr6:145116400-145122000	Weak transcription	Brain Anterior Caudate	brain
45	chr6:145116400-145125800	Weak transcription	Fetal Muscle Leg	muscle
46	chr6:145116400-145126600	Weak transcription	Fetal Intestine Large	intestine
47	chr6:145116400-145155600	Weak transcription	Stomach Smooth Muscle	stomach
48	chr6:145116400-145169000	Weak transcription	Rectal Smooth Muscle	rectum
49	chr6:145117000-145120600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr6:145117200-145120200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links