Variant report

Variant	rs2689091
Chromosome Location	chr6:35017003-35017004
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:35016131..35018255-chr6:35020438..35022614,2	MCF-7	breast:
2	chr6:35008594..35011463-chr6:35016010..35018720,2	MCF-7	breast:
3	chr6:35016477..35017231-chr6:35208580..35209106,2	MCF-7	breast:
4	chr6:35002495..35005140-chr6:35015377..35017563,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10947537	1.00[ASW][hapmap];0.85[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap]
rs12525532	0.91[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs12661389	1.00[ASW][hapmap];0.81[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13210323	0.84[CHD][hapmap]
rs1535815	1.00[ASW][hapmap];0.85[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2257663	0.92[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2494099	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2494100	0.88[CEU][hapmap];0.89[CHB][hapmap];0.80[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2689094	0.88[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2689096	0.80[JPT][hapmap]
rs2762335	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2762337	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2762338	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2762339	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2762340	0.83[CHB][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2762343	0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap]
rs2762345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2820223	0.82[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2820226	0.95[CEU][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2820228	0.85[CEU][hapmap];0.89[CHB][hapmap];0.80[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2820232	1.00[ASW][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.96[ASN][1000 genomes]
rs2820233	0.94[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs2820234	0.94[ASN][1000 genomes]
rs2820240	0.84[JPT][hapmap]
rs3823438	0.90[JPT][hapmap]
rs820076	0.81[GIH][hapmap]
rs820084	0.81[GIH][hapmap]
rs820089	0.81[GIH][hapmap]
rs847850	0.84[JPT][hapmap]
rs847852	1.00[ASW][hapmap]
rs847858	0.85[JPT][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	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2689091	HNF1B	trans	lymphoblastoid	seeQTL
rs2689091	C11orf9	trans	lymphoblastoid	seeQTL
rs2689091	NUDT3	cis	parietal	SCAN
rs2689091	ANKS1A	cis	cerebellum	SCAN
rs2689091	ANKS1A	cis	parietal	SCAN
rs2689091	HCK	trans	lymphoblastoid	seeQTL
rs2689091	TNFRSF21	trans	lymphoblastoid	seeQTL
rs2689091	CRIM1	trans	lymphoblastoid	seeQTL
rs2689091	CDKN1A	cis	cerebellum	SCAN
rs2689091	F13A1	trans	lymphoblastoid	seeQTL
rs2689091	HEY1	trans	lymphoblastoid	seeQTL
rs2689091	SHOX2	trans	lymphoblastoid	seeQTL
rs2689091	GRM4	cis	cerebellum	SCAN
rs2689091	RBPMS	trans	lymphoblastoid	seeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34994600-35036000	Weak transcription	K562	blood
2	chr6:35009000-35018800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr6:35009800-35018800	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr6:35010000-35017200	Enhancers	H1 Cell Line	embryonic stem cell
5	chr6:35010000-35018200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr6:35010200-35017600	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr6:35010200-35018000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:35010400-35018600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:35010400-35019000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:35010600-35017200	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr6:35011000-35017600	Enhancers	Fetal Muscle Leg	muscle
12	chr6:35011000-35018000	Enhancers	Stomach Mucosa	stomach
13	chr6:35011000-35018400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:35011400-35018600	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr6:35011800-35018400	Enhancers	Fetal Kidney	kidney
16	chr6:35011800-35019400	Enhancers	Dnd41	blood
17	chr6:35012000-35018400	Enhancers	Duodenum Mucosa	Duodenum
18	chr6:35012000-35020000	Genic enhancers	Fetal Intestine Small	intestine
19	chr6:35012200-35019200	Enhancers	Fetal Lung	lung
20	chr6:35012200-35019200	Enhancers	Fetal Thymus	thymus
21	chr6:35012800-35017800	Enhancers	Small Intestine	intestine
22	chr6:35013000-35018000	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr6:35013200-35018600	Weak transcription	HepG2	liver
24	chr6:35013800-35018800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:35014200-35017400	Enhancers	NHDF-Ad	bronchial
26	chr6:35014400-35017400	Enhancers	NHLF	lung
27	chr6:35014400-35019200	Enhancers	Placenta	Placenta
28	chr6:35014600-35017200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr6:35014600-35017800	Enhancers	Fetal Heart	heart
30	chr6:35014600-35019400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:35014600-35022200	Weak transcription	NHEK	skin
32	chr6:35014800-35018400	Enhancers	Spleen	Spleen
33	chr6:35014800-35021200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:35015000-35017400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr6:35015000-35018200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr6:35015000-35018200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:35015000-35018600	Enhancers	Right Ventricle	heart
38	chr6:35015000-35018800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr6:35015000-35018800	Enhancers	Ovary	ovary
40	chr6:35015000-35019000	Enhancers	Aorta	Aorta
41	chr6:35015200-35017400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
42	chr6:35015200-35017400	Enhancers	Gastric	stomach
43	chr6:35015200-35018600	Enhancers	Colonic Mucosa	Colon
44	chr6:35015200-35018600	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr6:35015200-35018800	Enhancers	Right Atrium	heart
46	chr6:35015200-35021800	Enhancers	Left Ventricle	heart
47	chr6:35015600-35017400	Enhancers	H9 Cell Line	embryonic stem cell
48	chr6:35015600-35017400	Flanking Active TSS	Brain Hippocampus Middle	brain
49	chr6:35015600-35017400	Flanking Active TSS	Brain Substantia Nigra	brain
50	chr6:35015600-35017800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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