Variant report

Variant	rs3778504
Chromosome Location	chr6:44189200-44189201
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	chr6:44188987-44189712	HepG2	liver:	n/a	chr6:44189070-44189081
2	ZNF143	chr6:44189020-44189616	Hela-S3	cervix:	n/a	n/a
3	CUX1	chr6:44189053-44189208	K562	blood:	n/a	n/a
4	MYC	chr6:44189011-44189630	NB4	blood:	n/a	chr6:44189070-44189081
5	POLR2A	chr6:44188973-44189760	ECC-1	luminal epithelium:	n/a	n/a
6	MYC	chr6:44188955-44189676	MCF10A-Er-Src	breast:	n/a	chr6:44189070-44189081
7	MAX	chr6:44188880-44189763	ECC-1	luminal epithelium:	n/a	chr6:44189070-44189081
8	MXI1	chr6:44189040-44189673	Hela-S3	cervix:	n/a	n/a
9	CTCF	chr6:44189200-44189648	MCF-7	breast:	n/a	chr6:44189443-44189461 chr6:44189446-44189455 chr6:44189446-44189459
10	POLR2A	chr6:44189092-44189312	GM12878	blood:	n/a	n/a
11	STAT3	chr6:44188979-44189238	MCF10A-Er-Src	breast:	n/a	n/a
12	RAD21	chr6:44189195-44189737	A549	lung:	n/a	chr6:44189444-44189463 chr6:44189449-44189459
13	POLR2A	chr6:44189143-44190361	HUVEC	blood vessel:	n/a	n/a
14	TEAD4	chr6:44188914-44189771	ECC-1	luminal epithelium:	n/a	n/a
15	MXI1	chr6:44188927-44189543	GM12878	blood:	n/a	n/a
16	MAFK	chr6:44189187-44189643	Hela-S3	cervix:	n/a	n/a
17	MAX	chr6:44188868-44189834	ECC-1	luminal epithelium:	n/a	chr6:44189070-44189081 chr6:44189804-44189814
18	MBD4	chr6:44188986-44189640	HepG2	liver:	n/a	n/a
19	ELF1	chr6:44188983-44189921	GM12878	blood:	n/a	n/a
20	TBP	chr6:44188977-44189228	GM12878	blood:	n/a	n/a
21	STAT1	chr6:44188990-44189536	GM12878	blood:	n/a	n/a
22	CTCF	chr6:44189049-44189240	GM19239	blood:	n/a	n/a
23	CTCF	chr6:44189188-44189669	HepG2	liver:	n/a	chr6:44189443-44189461 chr6:44189446-44189455 chr6:44189446-44189459
24	POLR2A	chr6:44189050-44189795	Hela-S3	cervix:	n/a	n/a
25	MYBL2	chr6:44189094-44189696	HepG2	liver:	n/a	n/a
26	POLR2A	chr6:44188940-44189406	GM12878	blood:	n/a	n/a
27	NR2F2	chr6:44188835-44189975	K562	blood:	n/a	n/a
28	EP300	chr6:44188973-44189516	HepG2	liver:	n/a	n/a
29	FOXM1	chr6:44189170-44189650	GM12878	blood:	n/a	n/a
30	BHLHE40	chr6:44189050-44189647	K562	blood:	n/a	chr6:44189447-44189463
31	POLR2A	chr6:44189071-44189977	PANC-1	pancreas:	n/a	n/a
32	NFIC	chr6:44188931-44189235	HepG2	liver:	n/a	n/a
33	MAX	chr6:44188916-44189680	K562	blood:	n/a	chr6:44189070-44189081
34	EP300	chr6:44188965-44189618	GM12878	blood:	n/a	n/a
35	JUND	chr6:44189099-44189606	K562	blood:	n/a	n/a
36	TCF12	chr6:44188952-44190002	ECC-1	luminal epithelium:	n/a	n/a
37	POLR2A	chr6:44188904-44190019	HUVEC	blood vessel:	n/a	n/a
38	NFIC	chr6:44188878-44190027	ECC-1	luminal epithelium:	n/a	chr6:44189508-44189525 chr6:44189508-44189524
39	RAD21	chr6:44189105-44189639	GM12878	blood:	n/a	chr6:44189444-44189463 chr6:44189449-44189459
40	POLR2A	chr6:44189073-44189778	Hela-S3	cervix:	n/a	n/a
41	EP300	chr6:44188795-44190010	ECC-1	luminal epithelium:	n/a	chr6:44189841-44189855
42	EP300	chr6:44188959-44189278	GM12878	blood:	n/a	n/a
43	MAX	chr6:44188920-44189831	A549	lung:	n/a	chr6:44189070-44189081 chr6:44189804-44189814
44	RCOR1	chr6:44189165-44189640	GM12878	blood:	n/a	n/a
45	TCF3	chr6:44188973-44189244	GM12878	blood:	n/a	n/a
46	MXI1	chr6:44188737-44190157	SK-N-SH	brain:	n/a	n/a
47	USF2	chr6:44188954-44189282	HepG2	liver:	n/a	n/a
48	BHLHE40	chr6:44188919-44189659	GM12878	blood:	n/a	chr6:44189447-44189463
49	MAZ	chr6:44189001-44189667	GM12878	blood:	n/a	chr6:44189070-44189081
50	RFX5	chr6:44189060-44189689	GM12878	blood:	n/a	chr6:44189572-44189580 chr6:44189459-44189475

No.	Distal block	Cell Line	Cell type
1	chr6:44092682..44101478-chr6:44189085..44198306,11	K562	blood:
2	chr6:44187521..44192952-chr6:44212221..44217106,13	MCF-7	breast:
3	chr6:44188998..44189909-chr6:44204941..44206651,4	K562	blood:
4	chr6:44188965..44189915-chr6:44201606..44202486,3	MCF-7	breast:
5	chr6:44145817..44148268-chr6:44187736..44189431,2	K562	blood:

Variant related genes	Relation type
SLC29A1	TF binding region
ENSG00000137216	Chromatin interaction
ENSG00000096384	Chromatin interaction
ENSG00000180992	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs73733871	1.00[EUR][1000 genomes]
rs9394996	1.00[TSI][hapmap]

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	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	201 gene(s)	inside rSNPs	diseases
2	nsv885851	chr6:44178471-44240559	Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
3	nsv885852	chr6:44185901-44222718	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:137 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44187200-44189600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:44187400-44189400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr6:44187400-44190600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr6:44187600-44189200	Weak transcription	Small Intestine	intestine
5	chr6:44187600-44189400	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr6:44187800-44189200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr6:44187800-44189600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr6:44187800-44190400	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr6:44187800-44190600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr6:44187800-44190600	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr6:44187800-44190600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:44187800-44190600	Enhancers	Fetal Thymus	thymus
13	chr6:44188000-44189200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:44188000-44189200	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr6:44188000-44189200	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr6:44188000-44189400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:44188000-44189400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr6:44188000-44189400	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr6:44188000-44189400	Weak transcription	Primary T cells from cord blood	blood
20	chr6:44188000-44189400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr6:44188000-44189400	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr6:44188000-44189400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr6:44188000-44189400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr6:44188000-44189400	Enhancers	Fetal Stomach	stomach
25	chr6:44188000-44189600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr6:44188000-44189600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr6:44188000-44189600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:44188000-44189600	Weak transcription	Aorta	Aorta
29	chr6:44188000-44189800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr6:44188000-44190400	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr6:44188000-44190600	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr6:44188000-44190600	Enhancers	Fetal Heart	heart
33	chr6:44188000-44190600	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr6:44188000-44190600	Enhancers	Fetal Muscle Leg	muscle
35	chr6:44188000-44190600	Enhancers	Placenta	Placenta
36	chr6:44188000-44190600	Enhancers	Thymus	Thymus
37	chr6:44188000-44190800	Enhancers	Liver	Liver
38	chr6:44188000-44190800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr6:44188000-44191000	Enhancers	Stomach Mucosa	stomach
40	chr6:44188000-44191800	Weak transcription	Fetal Kidney	kidney
41	chr6:44188200-44189200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr6:44188200-44189200	Enhancers	Fetal Muscle Trunk	muscle
43	chr6:44188200-44189200	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr6:44188200-44189400	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr6:44188200-44189400	Weak transcription	Primary B cells from cord blood	blood
46	chr6:44188200-44189600	Enhancers	Colon Smooth Muscle	Colon
47	chr6:44188200-44189600	Enhancers	HUVEC	blood vessel
48	chr6:44188200-44190400	Enhancers	GM12878-XiMat	blood
49	chr6:44188200-44190800	Enhancers	Pancreas	Pancrea
50	chr6:44188600-44189400	Enhancers	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links