Variant report

Variant	rs9295134
Chromosome Location	chr6:161450528-161450529
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	RUNX3	chr6:161449901-161451198	GM12878	blood:	n/a	chr6:161450380-161450389 chr6:161450380-161450389
2	CEBPB	chr6:161449972-161451033	GM12878	blood:	n/a	n/a
3	TBL1XR1	chr6:161449848-161451089	GM12878	blood:	n/a	n/a
4	POU2F2	chr6:161450437-161450857	GM12891	blood:	n/a	chr6:161450622-161450634 chr6:161450625-161450632 chr6:161450620-161450638 chr6:161450624-161450633 chr6:161450624-161450635 chr6:161450618-161450640 chr6:161450621-161450636 chr6:161450624-161450634
5	RCOR1	chr6:161450063-161450968	GM12878	blood:	n/a	n/a
6	SMC3	chr6:161449904-161450725	GM12878	blood:	n/a	n/a
7	POU2F2	chr6:161450440-161450867	GM12878	blood:	n/a	chr6:161450622-161450634 chr6:161450625-161450632 chr6:161450620-161450638 chr6:161450624-161450633 chr6:161450624-161450635 chr6:161450618-161450640 chr6:161450621-161450636 chr6:161450624-161450634
8	FOXM1	chr6:161450042-161450984	GM12878	blood:	n/a	n/a
9	POLR2A	chr6:161450356-161450857	GM12878	blood:	n/a	n/a
10	MTA3	chr6:161449852-161450941	GM12878	blood:	n/a	n/a
11	MEF2C	chr6:161449994-161450881	GM12878	blood:	n/a	chr6:161450532-161450548
12	CUX1	chr6:161449712-161450857	GM12878	blood:	n/a	n/a
13	CREB1	chr6:161450031-161451007	GM12878	blood:	n/a	n/a
14	EP300	chr6:161449870-161451067	GM12878	blood:	n/a	n/a
15	MEF2A	chr6:161450110-161450695	SK-N-SH	brain:	n/a	chr6:161450532-161450548
16	EBF1	chr6:161450054-161451220	GM12878	blood:	n/a	chr6:161450487-161450496 chr6:161450486-161450496
17	STAT5A	chr6:161450174-161450909	GM12878	blood:	n/a	n/a
18	POLR2A	chr6:161450477-161450885	GM12878	blood:	n/a	n/a
19	ELK1	chr6:161450293-161450694	GM12878	blood:	n/a	n/a
20	TBP	chr6:161449821-161451223	GM12878	blood:	n/a	n/a
21	BCLAF1	chr6:161450104-161450870	GM12878	blood:	n/a	n/a
22	STAT3	chr6:161450198-161450855	GM12878	blood:	n/a	n/a
23	ZNF384	chr6:161450119-161450685	GM12878	blood:	n/a	n/a
24	STAT1	chr6:161450297-161450758	GM12878	blood:	n/a	n/a
25	SP1	chr6:161450165-161450828	GM12878	blood:	n/a	chr6:161450286-161450300
26	EBF1	chr6:161450191-161450592	GM12878	blood:	n/a	chr6:161450487-161450496 chr6:161450486-161450496
27	STAT5A	chr6:161450153-161450702	GM12878	blood:	n/a	n/a
28	RUNX3	chr6:161450011-161450968	GM12878	blood:	n/a	chr6:161450380-161450389 chr6:161450380-161450389
29	CEBPB	chr6:161450378-161450980	IMR90	lung:	n/a	n/a
30	RELA	chr6:161450166-161450880	GM12878	blood:	n/a	n/a
31	CHD2	chr6:161450060-161450839	GM12878	blood:	n/a	n/a
32	MAZ	chr6:161450098-161450847	GM12878	blood:	n/a	n/a
33	BATF	chr6:161450165-161450828	GM12878	blood:	n/a	n/a
34	MEF2A	chr6:161450017-161450794	GM12878	blood:	n/a	chr6:161450532-161450548
35	NFIC	chr6:161450047-161450921	GM12878	blood:	n/a	n/a
36	BHLHE40	chr6:161450014-161451121	GM12878	blood:	n/a	n/a
37	NFIC	chr6:161449844-161451043	GM12878	blood:	n/a	n/a
38	NFATC1	chr6:161450068-161450796	GM12878	blood:	n/a	n/a
39	BCL11A	chr6:161450127-161450874	GM12878	blood:	n/a	n/a
40	FOXM1	chr6:161450018-161450963	GM12878	blood:	n/a	n/a
41	SP1	chr6:161450158-161450829	GM12878	blood:	n/a	chr6:161450286-161450300
42	RELA	chr6:161450061-161450856	GM18505	blood:	n/a	n/a
43	EBF1	chr6:161450247-161450678	GM12878	blood:	n/a	chr6:161450487-161450496 chr6:161450486-161450496
44	EP300	chr6:161450181-161450568	GM12878	blood:	n/a	n/a
45	BCL3	chr6:161450104-161450764	GM12878	blood:	n/a	n/a
46	POLR2A	chr6:161450480-161450767	GM12891	blood:	n/a	n/a
47	NFATC1	chr6:161450034-161450873	GM12878	blood:	n/a	n/a
48	MTA3	chr6:161450183-161450835	GM12878	blood:	n/a	n/a
49	EP300	chr6:161450028-161451338	GM12878	blood:	n/a	n/a
50	EP300	chr6:161450175-161450910	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:161429995..161433253-chr6:161449573..161453041,3	MCF-7	breast:

Variant related genes	Relation type
MAP3K4	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12110787	0.82[CHD][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12203648	0.84[CHB][hapmap];0.86[CHD][hapmap];0.87[LWK][hapmap]
rs13200744	0.95[CHB][hapmap];0.86[CHD][hapmap];0.89[ASN][1000 genomes]
rs1562027	1.00[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs1980328	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2314378	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3734461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3798915	0.97[EUR][1000 genomes]
rs4324757	0.83[LWK][hapmap]
rs4709485	0.89[CHB][hapmap];0.83[AFR][1000 genomes]
rs4709487	0.83[ASW][hapmap];0.91[LWK][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs4709488	0.83[CHB][hapmap]
rs589238	0.83[CHB][hapmap]
rs594555	0.88[CHB][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs594602	0.84[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs606817	0.89[AFR][1000 genomes]
rs625977	0.95[LWK][hapmap];0.80[MKK][hapmap];0.83[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes]
rs630006	1.00[CEU][hapmap];0.84[CHB][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs644486	0.89[AFR][1000 genomes]
rs6455702	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs671335	0.80[EUR][1000 genomes]
rs675457	0.86[AFR][1000 genomes]
rs6901173	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6901968	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6905734	0.86[YRI][hapmap]
rs6913867	0.84[CHB][hapmap]
rs705826	0.87[AFR][1000 genomes]
rs7746515	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7756711	0.84[CHB][hapmap]
rs9295138	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9347478	0.84[CHB][hapmap];0.86[CHD][hapmap];0.87[LWK][hapmap]
rs9355327	1.00[CEU][hapmap];0.84[CHB][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9355870	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9365246	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9456620	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9458102	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030045	chr6:161359075-161562255	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv886817	chr6:161371621-161846654	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	esv3381361	chr6:161373617-161864101	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1023982	chr6:161382188-161549831	Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking 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	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:161414200-161458200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr6:161414400-161469600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr6:161414600-161457400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr6:161416600-161475200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr6:161428600-161455800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr6:161432200-161451200	Weak transcription	NHEK	skin
7	chr6:161432600-161455400	Weak transcription	Fetal Intestine Large	intestine
8	chr6:161433000-161458000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:161433200-161459200	Weak transcription	Fetal Stomach	stomach
10	chr6:161433400-161455600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr6:161433400-161455800	Weak transcription	Fetal Muscle Leg	muscle
12	chr6:161433400-161455800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr6:161433400-161459000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr6:161433600-161458200	Weak transcription	Fetal Brain Female	brain
15	chr6:161433600-161459600	Weak transcription	Brain Germinal Matrix	brain
16	chr6:161433800-161451000	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr6:161434000-161455600	Weak transcription	Adipose Nuclei	Adipose
18	chr6:161434000-161459000	Weak transcription	Brain Hippocampus Middle	brain
19	chr6:161434800-161458200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr6:161435000-161452200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr6:161435000-161458000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr6:161435000-161458800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr6:161435000-161490400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr6:161435200-161454800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr6:161435200-161455800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr6:161436800-161455600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr6:161437000-161451200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr6:161437000-161451600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr6:161437000-161452800	Weak transcription	Primary T cells from cord blood	blood
30	chr6:161437400-161457600	Weak transcription	Liver	Liver
31	chr6:161437800-161451200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr6:161438000-161452400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr6:161439000-161454800	Weak transcription	Dnd41	blood
34	chr6:161439200-161458800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr6:161440200-161459200	Weak transcription	Placenta	Placenta
36	chr6:161440600-161459600	Weak transcription	Esophagus	oesophagus
37	chr6:161441200-161459800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr6:161442600-161459200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:161442800-161455600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr6:161442800-161459600	Weak transcription	Fetal Intestine Small	intestine
41	chr6:161442800-161463400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr6:161443600-161455600	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr6:161443800-161457800	Weak transcription	Primary B cells from cord blood	blood
44	chr6:161443800-161458000	Weak transcription	HepG2	liver
45	chr6:161443800-161459000	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr6:161443800-161459000	Weak transcription	Right Ventricle	heart
47	chr6:161443800-161462000	Weak transcription	Spleen	Spleen
48	chr6:161443800-161465600	Weak transcription	Right Atrium	heart
49	chr6:161443800-161478600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr6:161444000-161451600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links