Variant report

Variant	rs2269703
Chromosome Location	chr6:30658385-30658386
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	TAF1	chr6:30658326-30658612	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr6:30658269-30659156	HCT-116	colon:	n/a	n/a
3	MAZ	chr6:30658296-30659060	K562	blood:	n/a	chr6:30658547-30658557 chr6:30659019-30659030 chr6:30658847-30658857
4	POLR2A	chr6:30658263-30659124	K562	blood:	n/a	n/a
5	POLR2A	chr6:30657699-30659147	GM12878	blood:	n/a	n/a
6	NFATC1	chr6:30658239-30659303	GM12878	blood:	n/a	n/a
7	HEY1	chr6:30658259-30658694	K562	blood:	n/a	n/a
8	RUNX3	chr6:30658316-30659156	GM12878	blood:	n/a	n/a
9	POLR2A	chr6:30658193-30659195	SK-N-SH	brain:	n/a	n/a
10	PML	chr6:30658134-30659239	GM12878	blood:	n/a	n/a
11	SIN3AK20	chr6:30658182-30659093	K562	blood:	n/a	n/a
12	POLR2A	chr6:30658231-30658665	U87	brain:	n/a	n/a
13	POLR2A	chr6:30658146-30659171	GM12892	blood:	n/a	n/a
14	YY1	chr6:30658285-30659087	GM12878	blood:	n/a	n/a
15	MAX	chr6:30657673-30659090	K562	blood:	n/a	chr6:30658237-30658248 chr6:30658547-30658557 chr6:30659019-30659030 chr6:30658847-30658857
16	SIN3A	chr6:30658090-30659097	H1-hESC	embryonic stem cell:	n/a	chr6:30659019-30659028
17	WRNIP1	chr6:30658106-30658451	GM12878	blood:	n/a	n/a
18	TAF1	chr6:30658385-30659089	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr6:30652434-30659300	HUVEC	blood vessel:	n/a	n/a
20	IKZF1	chr6:30657882-30659072	GM12878	blood:	n/a	n/a
21	POLR2A	chr6:30657844-30659114	Hela-S3	cervix:	n/a	n/a
22	REST	chr6:30658199-30659334	H1-neurons	neurons:	n/a	n/a
23	POLR2A	chr6:30658358-30659029	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr6:30658368-30659316	HepG2	liver:	n/a	n/a
25	MXI1	chr6:30657614-30659658	SK-N-SH	brain:	n/a	n/a
26	SMC3	chr6:30658369-30659045	Hela-S3	cervix:	n/a	n/a
27	MAX	chr6:30658028-30659067	ECC-1	luminal epithelium:	n/a	chr6:30658237-30658248 chr6:30658547-30658557 chr6:30659019-30659030 chr6:30658847-30658857
28	MAX	chr6:30658039-30659170	ECC-1	luminal epithelium:	n/a	chr6:30658237-30658248 chr6:30658547-30658557 chr6:30659019-30659030 chr6:30658847-30658857
29	NFATC1	chr6:30658230-30658976	GM12878	blood:	n/a	n/a
30	POLR2A	chr6:30658187-30659219	Hela-S3	cervix:	n/a	n/a
31	NFIC	chr6:30658385-30659136	GM12878	blood:	n/a	n/a
32	TCF12	chr6:30658308-30659158	ECC-1	luminal epithelium:	n/a	n/a
33	POLR2A	chr6:30658304-30659108	GM12892	blood:	n/a	n/a
34	RELA	chr6:30658280-30659101	GM12891	blood:	n/a	n/a
35	POLR2A	chr6:30653392-30659188	GM12892	blood:	n/a	n/a
36	EP300	chr6:30658356-30658660	GM12878	blood:	n/a	n/a
37	STAT1	chr6:30658192-30659049	GM12878	blood:	n/a	n/a
38	SP1	chr6:30658367-30659181	A549	lung:	n/a	chr6:30658547-30658556 chr6:30658847-30658857 chr6:30658843-30658857 chr6:30658848-30658857 chr6:30658548-30658557 chr6:30658546-30658558 chr6:30658547-30658561 chr6:30658846-30658858 chr6:30658846-30658858 chr6:30658546-30658558 chr6:30658847-30658856 chr6:30658547-30658557
39	POLR2A	chr6:30658056-30659104	K562	blood:	n/a	n/a
40	TAF1	chr6:30658245-30659130	ECC-1	luminal epithelium:	n/a	n/a
41	POLR2A	chr6:30657593-30659058	K562	blood:	n/a	n/a
42	RAD21	chr6:30658355-30658538	K562	blood:	n/a	n/a
43	TBL1XR1	chr6:30658359-30659075	GM12878	blood:	n/a	n/a
44	POLR2A	chr6:30658257-30659108	GM12878	blood:	n/a	n/a
45	GTF2F1	chr6:30658262-30658818	K562	blood:	n/a	n/a
46	HCFC1	chr6:30658337-30659080	K562	blood:	n/a	n/a
47	MAX	chr6:30658008-30659094	SK-N-SH	brain:	n/a	chr6:30658237-30658248 chr6:30658547-30658557 chr6:30659019-30659030 chr6:30658847-30658857
48	RUNX3	chr6:30658319-30659129	GM12878	blood:	n/a	n/a
49	ELF1	chr6:30658333-30659088	K562	blood:	n/a	n/a
50	YY1	chr6:30658353-30659009	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:30652587..30660257-chr6:30673612..30681352,12	MCF-7	breast:
2	chr6:30643326..30660432-chr6:30681522..30696111,127	MCF-7	breast:
3	chr6:30634661..30668428-chr6:30680318..30698953,145	MCF-7	breast:
4	chr6:30580498..30587281-chr6:30649167..30662031,51	K562	blood:
5	chr6:30657201..30658778-chr6:30748296..30750541,2	K562	blood:
6	chr6:30658243..30658855-chr6:30684681..30685476,2	NB4	blood:
7	chr6:30582891..30586139-chr6:30656870..30660301,3	MCF-7	breast:
8	chr6:30657343..30659554-chr6:30673396..30677307,4	MCF-7	breast:

Variant related genes	Relation type
NRM	TF binding region
PPP1R18	TF binding region
ENSG00000137337	Chromatin interaction
ENSG00000228022	Chromatin interaction
ENSG00000204568	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000272540	Chromatin interaction
ENSG00000196230	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs17189246	0.88[ASN][1000 genomes]
rs2239887	0.88[ASN][1000 genomes]
rs2269708	0.88[ASN][1000 genomes]
rs28986466	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130663	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs41273001	0.88[ASN][1000 genomes]
rs57302671	0.88[ASN][1000 genomes]
rs73422011	0.85[ASN][1000 genomes]
rs73422013	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS 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	1012 gene(s)	inside rSNPs	diseases
4	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
5	nsv884086	chr6:30462084-30672757	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	798 gene(s)	inside rSNPs	diseases
6	nsv830626	chr6:30558064-30732905	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	406 gene(s)	inside rSNPs	diseases
7	nsv884094	chr6:30637998-30660611	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
8	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
9	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
10	nsv884095	chr6:30644987-30664567	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
11	nsv884096	chr6:30647979-30664567	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
12	nsv884097	chr6:30650378-30660611	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
13	nsv884098	chr6:30650378-30664567	Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
14	nsv884099	chr6:30652931-30660611	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2269703	LTB	cis	lymphoblastoid	seeQTL
rs2269703	TNF	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30655000-30658600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:30655000-30659200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
3	chr6:30655400-30658400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr6:30655600-30658400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:30655800-30658400	Flanking Active TSS	Brain Germinal Matrix	brain
6	chr6:30656000-30658400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:30656000-30658400	Enhancers	Primary T cells fromperipheralblood	blood
8	chr6:30656000-30658600	Weak transcription	Aorta	Aorta
9	chr6:30656600-30658400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:30656600-30658400	Enhancers	Spleen	Spleen
11	chr6:30656600-30659200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr6:30656800-30658400	Flanking Active TSS	Dnd41	blood
13	chr6:30656800-30659200	Flanking Active TSS	Primary B cells from cord blood	blood
14	chr6:30657000-30658400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:30657000-30658400	Flanking Active TSS	Stomach Smooth Muscle	stomach
16	chr6:30657200-30658400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:30657200-30658400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:30657200-30658400	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr6:30657200-30658600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
20	chr6:30657400-30658400	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr6:30657400-30658400	Flanking Active TSS	Colon Smooth Muscle	Colon
22	chr6:30657400-30658400	Flanking Active TSS	K562	blood
23	chr6:30657400-30658400	Flanking Active TSS	NH-A	brain
24	chr6:30657400-30658400	Flanking Active TSS	NHDF-Ad	bronchial
25	chr6:30657400-30658400	Flanking Active TSS	Osteobl	bone
26	chr6:30657400-30658600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr6:30657400-30659400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
28	chr6:30657400-30659600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:30657600-30658400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr6:30657600-30658400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:30657600-30658400	Flanking Active TSS	Fetal Lung	lung
32	chr6:30657600-30658400	Flanking Active TSS	Fetal Stomach	stomach
33	chr6:30657600-30658400	Flanking Active TSS	Rectal Smooth Muscle	rectum
34	chr6:30657600-30658400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr6:30657600-30658600	Flanking Active TSS	Primary B cells from peripheral blood	blood
36	chr6:30657600-30658600	Flanking Active TSS	Fetal Muscle Leg	muscle
37	chr6:30657600-30658600	Flanking Active TSS	Hela-S3	cervix
38	chr6:30657600-30658600	Flanking Active TSS	HMEC	breast
39	chr6:30657600-30659200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr6:30657600-30659600	Flanking Active TSS	Primary hematopoietic stem cells	blood
41	chr6:30657800-30658400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
42	chr6:30657800-30658400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr6:30657800-30658400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr6:30657800-30658400	Flanking Active TSS	Primary T cells from cord blood	blood
45	chr6:30657800-30658400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr6:30657800-30658400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr6:30657800-30658400	Flanking Active TSS	Brain Substantia Nigra	brain
48	chr6:30657800-30658400	Flanking Active TSS	Colonic Mucosa	Colon
49	chr6:30657800-30658400	Flanking Active TSS	Duodenum Mucosa	Duodenum
50	chr6:30657800-30658400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links