Variant report

Variant	rs2235418
Chromosome Location	chr6:11732823-11732824
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	MTA3	chr6:11730225-11733592	GM12878	blood:	n/a	n/a
2	TCF3	chr6:11732165-11732892	GM12878	blood:	n/a	n/a
3	SPI1	chr6:11732425-11732832	HL-60	blood:	n/a	n/a
4	POLR2A	chr6:11732502-11733494	GM12892	blood:	n/a	n/a
5	PAX5	chr6:11732303-11732851	GM12878	blood:	n/a	n/a
6	POLR2A	chr6:11732126-11733613	GM12892	blood:	n/a	n/a
7	ELF1	chr6:11732290-11732948	GM12878	blood:	n/a	n/a
8	MAX	chr6:11732342-11732966	GM12878	blood:	n/a	chr6:11732654-11732663 chr6:11732519-11732528
9	PAX5	chr6:11732443-11732844	GM12892	blood:	n/a	n/a
10	CHD1	chr6:11732157-11733026	GM12878	blood:	n/a	n/a
11	YY1	chr6:11732475-11732826	GM12892	blood:	n/a	n/a
12	NFATC1	chr6:11731956-11732923	GM12878	blood:	n/a	n/a
13	POLR2A	chr6:11732454-11732831	GM12878	blood:	n/a	n/a
14	BCL11A	chr6:11732094-11732861	GM12878	blood:	n/a	chr6:11732311-11732320
15	STAT5A	chr6:11731588-11733345	GM12878	blood:	n/a	chr6:11732990-11733002 chr6:11732311-11732322
16	MAX	chr6:11732039-11733102	NB4	blood:	n/a	chr6:11733061-11733068 chr6:11732654-11732663 chr6:11732519-11732528
17	IRF4	chr6:11732132-11732903	GM12878	blood:	n/a	n/a
18	FOXM1	chr6:11731884-11733029	GM12878	blood:	n/a	n/a
19	POLR2A	chr6:11730546-11733461	GM12878	blood:	n/a	n/a
20	NRF1	chr6:11732413-11732916	GM12878	blood:	n/a	n/a
21	RUNX3	chr6:11731726-11733545	GM12878	blood:	n/a	n/a
22	BCLAF1	chr6:11731982-11732930	GM12878	blood:	n/a	chr6:11732311-11732320
23	TCF3	chr6:11732156-11732827	GM12878	blood:	n/a	n/a
24	POLR2A	chr6:11732211-11732857	HL-60	blood:	n/a	n/a
25	EP300	chr6:11732127-11733063	GM12878	blood:	n/a	n/a
26	POLR2A	chr6:11732343-11733522	GM12891	blood:	n/a	n/a
27	EP300	chr6:11732127-11732936	GM12878	blood:	n/a	n/a
28	CREB1	chr6:11732212-11732940	GM12878	blood:	n/a	n/a
29	EBF1	chr6:11732213-11732932	GM12878	blood:	n/a	n/a
30	SPI1	chr6:11732143-11732840	GM12891	blood:	n/a	chr6:11732311-11732320
31	RCOR1	chr6:11732184-11733065	GM12878	blood:	n/a	n/a
32	BCLAF1	chr6:11732086-11732876	GM12878	blood:	n/a	chr6:11732311-11732320
33	YY1	chr6:11732166-11732870	GM12891	blood:	n/a	n/a
34	RELA	chr6:11732160-11733053	GM19193	blood:	n/a	n/a
35	POLR2A	chr6:11730647-11733571	GM12892	blood:	n/a	n/a
36	POLR2A	chr6:11732308-11733403	GM12891	blood:	n/a	n/a
37	YY1	chr6:11732307-11732906	GM12892	blood:	n/a	n/a
38	IRF4	chr6:11732091-11732996	GM12878	blood:	n/a	n/a
39	SPI1	chr6:11731931-11733088	GM12878	blood:	n/a	chr6:11732311-11732320
40	PAX5	chr6:11732116-11732981	GM12878	blood:	n/a	chr6:11732203-11732222
41	POLR2A	chr6:11730690-11733720	GM12892	blood:	n/a	n/a
42	NFIC	chr6:11731457-11733009	GM12878	blood:	n/a	chr6:11732741-11732758
43	MTA3	chr6:11730668-11733834	GM12878	blood:	n/a	n/a
44	BHLHE40	chr6:11732155-11733052	GM12878	blood:	n/a	n/a
45	TCF12	chr6:11732338-11732866	GM12878	blood:	n/a	n/a
46	MEF2C	chr6:11732037-11732971	GM12878	blood:	n/a	chr6:11732519-11732527 chr6:11732443-11732464 chr6:11732310-11732318 chr6:11732443-11732464 chr6:11732447-11732458 chr6:11732448-11732457 chr6:11732445-11732459
47	RELA	chr6:11732141-11732831	GM12878	blood:	n/a	n/a
48	POU2F2	chr6:11732261-11732928	GM12878	blood:	n/a	n/a
49	TBL1XR1	chr6:11732085-11733069	GM12878	blood:	n/a	n/a
50	MEF2A	chr6:11731980-11732843	GM12878	blood:	n/a	chr6:11732519-11732527 chr6:11732443-11732464 chr6:11732310-11732318 chr6:11732443-11732464 chr6:11732447-11732458 chr6:11732448-11732457 chr6:11732445-11732459

No.	Distal block	Cell Line	Cell type
1	chr6:11722035..11725191-chr6:11730801..11735491,4	K562	blood:
2	chr6:11726535..11729461-chr6:11731362..11733356,2	MCF-7	breast:
3	chr6:11732175..11734663-chr6:11982258..11984188,2	MCF-7	breast:
4	chr6:11731733..11734169-chr6:11735074..11737583,2	K562	blood:
5	chr6:11729664..11733352-chr6:11734064..11737412,4	K562	blood:
6	chr6:11723063..11725185-chr6:11732645..11735491,2	K562	blood:

Variant related genes	Relation type
ADTRP	TF binding region
ENSG00000111863	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs2235392	0.82[CEU][hapmap]
rs2235413	0.82[CHD][hapmap]
rs2235414	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2235419	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2294419	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2294421	0.80[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2294425	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2294426	0.95[MEX][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2294427	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2294428	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4713834	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4713849	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs760789	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs932343	0.81[CHD][hapmap]
rs932345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9348963	0.95[MEX][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9366877	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9368855	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9394285	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	esv2758036	chr6:11679753-11822351	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2759407	chr6:11679753-11822351	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv428470	chr6:11686198-11747850	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv462637	chr6:11710554-11733777	Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv600990	chr6:11710554-11733777	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2235418	C6orf105	cis	multi-tissue	Pritchard
rs2235418	C6orf105	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11719400-11762200	Weak transcription	Colonic Mucosa	Colon
2	chr6:11723200-11738400	Weak transcription	HMEC	breast
3	chr6:11723600-11744200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:11725200-11748600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:11726400-11744600	Weak transcription	Right Atrium	heart
6	chr6:11727000-11734000	Enhancers	Primary hematopoietic stem cells	blood
7	chr6:11729000-11733000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr6:11729400-11733200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr6:11729400-11733200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr6:11729600-11733200	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr6:11729600-11734000	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr6:11729800-11733200	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr6:11730200-11736200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:11730600-11733200	Enhancers	Fetal Thymus	thymus
15	chr6:11730800-11733400	Enhancers	Adipose Nuclei	Adipose
16	chr6:11731000-11733200	Enhancers	Gastric	stomach
17	chr6:11731200-11733000	Flanking Active TSS	GM12878-XiMat	blood
18	chr6:11731200-11733200	Enhancers	Pancreas	Pancrea
19	chr6:11731400-11733000	Enhancers	Duodenum Mucosa	Duodenum
20	chr6:11731400-11734800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr6:11731600-11733000	Enhancers	Muscle Satellite Cultured Cells	--
22	chr6:11731600-11733200	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr6:11731600-11733200	Enhancers	HSMMtube	muscle
24	chr6:11731600-11733200	Enhancers	NHLF	lung
25	chr6:11731600-11733600	Enhancers	Fetal Brain Male	brain
26	chr6:11731800-11733000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr6:11731800-11733000	Enhancers	Fetal Muscle Leg	muscle
28	chr6:11731800-11733000	Enhancers	HSMM	muscle
29	chr6:11731800-11733400	Enhancers	Primary T cells from cord blood	blood
30	chr6:11732000-11735800	Weak transcription	Spleen	Spleen
31	chr6:11732000-11737400	Weak transcription	Ovary	ovary
32	chr6:11732200-11733200	Enhancers	Primary B cells from peripheral blood	blood
33	chr6:11732200-11733600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:11732400-11733000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr6:11732400-11733000	Enhancers	Brain Cingulate Gyrus	brain
36	chr6:11732400-11733400	Enhancers	Esophagus	oesophagus
37	chr6:11732400-11733600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:11732400-11733600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr6:11732400-11734200	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr6:11732400-11736200	Strong transcription	NHEK	skin
41	chr6:11732400-11744800	Weak transcription	Fetal Intestine Small	intestine
42	chr6:11732400-11750400	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr6:11732600-11733000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr6:11732600-11733000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
45	chr6:11732600-11733000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr6:11732600-11733000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr6:11732600-11733000	Enhancers	Fetal Muscle Trunk	muscle
48	chr6:11732600-11733200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr6:11732600-11733200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
50	chr6:11732600-11733200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links