Variant report

Variant	rs6664900
Chromosome Location	chr1:209941383-209941384
allele	C/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	MAX	chr1:209941095-209944027	NB4	blood:	n/a	chr1:209943038-209943048 chr1:209943557-209943567
2	POLR2A	chr1:209940700-209952492	GM12891	blood:	n/a	n/a
3	MYC	chr1:209941106-209942318	NB4	blood:	n/a	n/a
4	MAZ	chr1:209941196-209943615	GM12878	blood:	n/a	chr1:209943038-209943048 chr1:209943557-209943567
5	RUNX3	chr1:209941077-209941433	GM12878	blood:	n/a	chr1:209941262-209941271 chr1:209941262-209941271
6	POLR2A	chr1:209941117-209946709	GM18505	blood:	n/a	n/a
7	FOXM1	chr1:209941221-209942189	GM12878	blood:	n/a	n/a
8	NFIC	chr1:209941254-209942168	GM12878	blood:	n/a	n/a
9	TBL1XR1	chr1:209941228-209943259	GM12878	blood:	n/a	n/a
10	RELA	chr1:209941085-209943380	GM12891	blood:	n/a	n/a
11	RELA	chr1:209941196-209943211	GM10847	blood:	n/a	n/a
12	RUNX3	chr1:209941047-209941463	GM12878	blood:	n/a	chr1:209941262-209941271 chr1:209941262-209941271
13	POLR2A	chr1:209941182-209943356	NB4	blood:	n/a	n/a
14	SPI1	chr1:209941015-209941528	HL-60	blood:	n/a	n/a
15	IKZF1	chr1:209941184-209943507	GM12878	blood:	n/a	chr1:209942495-209942507
16	TBP	chr1:209941373-209943304	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:209940844..209943415-chr1:209955888..209958090,3	K562	blood:
2	chr1:209940429..209942619-chr1:209957623..209959222,2	MCF-7	breast:

Variant related genes	Relation type
TRAF3IP3	TF binding region
ENSG00000162757	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11803939	1.00[EUR][1000 genomes]
rs57565140	1.00[EUR][1000 genomes]
rs59116143	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59362743	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7545918	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1006632	chr1:209886202-209970355	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv4343	chr1:209929932-209974877	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209921800-209942000	Weak transcription	Pancreas	Pancrea
2	chr1:209931000-209941800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:209931000-209942000	Weak transcription	Esophagus	oesophagus
4	chr1:209931000-209943200	Weak transcription	Lung	lung
5	chr1:209931000-209943600	Weak transcription	Gastric	stomach
6	chr1:209932200-209941400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr1:209932200-209941800	Weak transcription	Colonic Mucosa	Colon
8	chr1:209932200-209942000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:209933800-209941600	Weak transcription	Fetal Muscle Leg	muscle
10	chr1:209934000-209941600	Weak transcription	Colon Smooth Muscle	Colon
11	chr1:209934600-209941600	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr1:209934800-209941800	Weak transcription	Right Ventricle	heart
13	chr1:209934800-209942000	Weak transcription	Brain Substantia Nigra	brain
14	chr1:209934800-209942000	Weak transcription	Right Atrium	heart
15	chr1:209937000-209941600	Weak transcription	Spleen	Spleen
16	chr1:209938800-209941400	Enhancers	Fetal Intestine Large	intestine
17	chr1:209939200-209941400	Genic enhancers	GM12878-XiMat	blood
18	chr1:209939200-209941600	Enhancers	Fetal Intestine Small	intestine
19	chr1:209939400-209941400	Genic enhancers	Primary B cells from peripheral blood	blood
20	chr1:209939800-209941600	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
21	chr1:209940000-209941400	Enhancers	Primary hematopoietic stem cells	blood
22	chr1:209940000-209941400	Weak transcription	Duodenum Mucosa	Duodenum
23	chr1:209940000-209941800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:209940600-209941800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
25	chr1:209940600-209942800	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
26	chr1:209940600-209943600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:209940600-209944200	Flanking Active TSS	Dnd41	blood
28	chr1:209940800-209941400	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
29	chr1:209940800-209941600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:209940800-209941600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr1:209940800-209941600	Flanking Active TSS	Thymus	Thymus
32	chr1:209940800-209941800	Flanking Active TSS	Primary T cells from cord blood	blood
33	chr1:209940800-209942800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
34	chr1:209940800-209943800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:209940800-209943800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr1:209940800-209944000	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr1:209940800-209944000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:209940800-209944000	Enhancers	HMEC	breast
39	chr1:209940800-209946200	Enhancers	Fetal Stomach	stomach
40	chr1:209941000-209941400	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
41	chr1:209941000-209941400	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:209941000-209941400	Weak transcription	NHEK	skin
43	chr1:209941000-209941600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr1:209941000-209941800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr1:209941000-209941800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
46	chr1:209941000-209941800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr1:209941000-209941800	Enhancers	Stomach Smooth Muscle	stomach
48	chr1:209941000-209942000	Flanking Active TSS	Fetal Thymus	thymus
49	chr1:209941000-209942200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
50	chr1:209941000-209942200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links