Variant report

Variant	rs9469987
Chromosome Location	chr6:35277396-35277397
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	POLR2A	chr6:35277312-35277530	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:35277272-35277955	HL-60	blood:	n/a	n/a
3	POLR2A	chr6:35277265-35277664	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:35270811..35278072-chr6:35434777..35439344,8	MCF-7	breast:
2	chr6:35275753..35280306-chr6:35283312..35286403,4	MCF-7	breast:

Variant related genes	Relation type
DEF6	TF binding region
ENSG00000198755	Chromatin interaction
ENSG00000023892	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12332985	0.86[YRI][hapmap]
rs16868709	0.86[YRI][hapmap]
rs16874062	0.93[YRI][hapmap]
rs16874262	0.93[YRI][hapmap]
rs57127611	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60812576	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61534122	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6906117	0.87[YRI][hapmap]
rs9296145	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9462061	0.85[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9462070	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9462078	0.81[YRI][hapmap];0.88[AFR][1000 genomes]
rs9469952	1.00[AMR][1000 genomes]
rs9469962	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9469973	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9469974	1.00[AMR][1000 genomes]
rs9469977	0.89[YRI][hapmap]
rs9469983	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9469984	0.81[AFR][1000 genomes]
rs9469993	0.93[YRI][hapmap]
rs9470003	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9470004	0.86[YRI][hapmap]
rs9470005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9470011	0.86[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758047	chr6:35168116-35291002	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	esv2759419	chr6:35168116-35291002	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35265200-35285600	Weak transcription	Brain Substantia Nigra	brain
2	chr6:35266600-35279800	Weak transcription	Fetal Stomach	stomach
3	chr6:35266800-35277400	Weak transcription	Pancreas	Pancrea
4	chr6:35268600-35278600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr6:35270600-35277400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:35270600-35278200	Weak transcription	Esophagus	oesophagus
7	chr6:35271000-35277400	Weak transcription	Spleen	Spleen
8	chr6:35271200-35277400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:35271200-35278000	Weak transcription	Right Atrium	heart
10	chr6:35271400-35277600	Weak transcription	Colonic Mucosa	Colon
11	chr6:35271400-35279800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr6:35271400-35285000	Weak transcription	HepG2	liver
13	chr6:35271600-35278000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr6:35271600-35285200	Weak transcription	Fetal Intestine Large	intestine
15	chr6:35271600-35285600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr6:35271800-35278400	Genic enhancers	Primary T cells fromperipheralblood	blood
17	chr6:35272400-35277800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr6:35272400-35278000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr6:35272400-35278200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr6:35272400-35279200	Weak transcription	Adipose Nuclei	Adipose
21	chr6:35272400-35284600	Weak transcription	HMEC	breast
22	chr6:35272400-35285400	Weak transcription	Gastric	stomach
23	chr6:35272600-35280200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr6:35273000-35277600	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr6:35273200-35277800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
26	chr6:35273200-35278200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr6:35274200-35277600	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr6:35274400-35277400	Strong transcription	Primary hematopoietic stem cells	blood
29	chr6:35274400-35277800	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr6:35274400-35277800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr6:35274800-35278800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr6:35275000-35279200	Enhancers	Placenta	Placenta
33	chr6:35275400-35278000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:35275600-35277600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr6:35275600-35278400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr6:35276000-35278000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr6:35276000-35293800	Weak transcription	K562	blood
38	chr6:35276600-35277400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr6:35276600-35277800	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr6:35276600-35279200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr6:35276800-35277600	Genic enhancers	GM12878-XiMat	blood
42	chr6:35276800-35278200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
43	chr6:35276800-35278400	Genic enhancers	Primary B cells from cord blood	blood
44	chr6:35276800-35278600	Genic enhancers	Rectal Mucosa Donor 29	rectum
45	chr6:35276800-35278800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr6:35276800-35279000	Genic enhancers	Thymus	Thymus
47	chr6:35276800-35279200	Genic enhancers	Primary B cells from peripheral blood	blood
48	chr6:35276800-35279200	Genic enhancers	Fetal Thymus	thymus
49	chr6:35276800-35279800	Genic enhancers	Dnd41	blood
50	chr6:35276800-35280600	Strong transcription	Fetal Intestine Small	intestine

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