Variant report

Variant	rs17397449
Chromosome Location	chr2:48644342-48644343
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:48337553..48343006-chr2:48644200..48649231,9	MCF-7	breast:
2	chr2:48643733..48645696-chr2:48650632..48652708,2	K562	blood:
3	chr2:48336673..48339163-chr2:48642028..48644836,2	K562	blood:
4	chr2:48641901..48644739-chr2:48646186..48647771,2	K562	blood:
5	chr2:48540493..48542753-chr2:48643021..48644548,2	K562	blood:

Variant related genes	Relation type
ENSG00000170802	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10182093	0.90[EUR][1000 genomes]
rs10191938	0.90[EUR][1000 genomes]
rs10195717	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs10197359	0.91[EUR][1000 genomes]
rs10454134	1.00[YRI][hapmap]
rs10495951	1.00[YRI][hapmap]
rs10495952	1.00[YRI][hapmap]
rs11674217	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs11674317	0.80[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11675947	0.80[AMR][1000 genomes]
rs11676078	0.84[EUR][1000 genomes]
rs11676925	0.80[AMR][1000 genomes]
rs11677205	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11678825	0.85[EUR][1000 genomes]
rs11678934	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs11679518	0.80[AMR][1000 genomes]
rs11679685	0.93[EUR][1000 genomes]
rs11680968	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11682838	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11683202	0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs11687276	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11687461	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11687771	0.82[CEU][hapmap]
rs11687851	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11688481	1.00[YRI][hapmap]
rs11689285	0.88[CEU][hapmap]
rs11690526	0.88[CEU][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap]
rs11691302	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11691407	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11692537	0.88[CEU][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs11694094	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11694955	0.91[EUR][1000 genomes]
rs13398456	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs28505584	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2937	0.88[CEU][hapmap]
rs4364065	0.93[EUR][1000 genomes]
rs6747738	0.88[CEU][hapmap]
rs72889641	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7573281	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7584796	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs952468	1.00[CEU][hapmap]

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	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv581775	chr2:48619869-48714938	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv518718	chr2:48624007-48650308	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	esv3343616	chr2:48644143-48644615	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17397449	MSH6	cis	lymphoblastoid	seeQTL
rs17397449	STON1-GTF2A1L	cis	cerebellum	SCAN
rs17397449	KLRAQ1	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48639600-48645200	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr2:48639600-48647400	Enhancers	Liver	Liver
3	chr2:48640000-48646200	Enhancers	Fetal Intestine Small	intestine
4	chr2:48640400-48647600	Weak transcription	Colon Smooth Muscle	Colon
5	chr2:48640400-48647600	Weak transcription	Ovary	ovary
6	chr2:48640600-48647800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:48641000-48647400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr2:48642400-48644800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:48642400-48647600	Weak transcription	Pancreas	Pancrea
10	chr2:48642600-48644600	Enhancers	Brain Substantia Nigra	brain
11	chr2:48642600-48645200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:48642800-48647400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:48642800-48647400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr2:48642800-48647400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:48642800-48647400	Weak transcription	NH-A	brain
16	chr2:48642800-48647600	Weak transcription	Osteobl	bone
17	chr2:48643000-48644400	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr2:48643000-48646200	Weak transcription	Spleen	Spleen
19	chr2:48643000-48647200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:48643000-48647600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr2:48643000-48647600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr2:48643000-48647600	Weak transcription	NHLF	lung
23	chr2:48643200-48644800	Enhancers	Brain Cingulate Gyrus	brain
24	chr2:48643200-48647400	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr2:48643200-48647600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr2:48643200-48647600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:48643200-48647800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr2:48643400-48644400	Enhancers	Brain Anterior Caudate	brain
29	chr2:48643400-48647000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:48643400-48647000	Enhancers	Brain Hippocampus Middle	brain
31	chr2:48643400-48647600	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr2:48643400-48647800	Weak transcription	Fetal Kidney	kidney
33	chr2:48643600-48644600	Weak transcription	Fetal Intestine Large	intestine
34	chr2:48643600-48644600	Weak transcription	Fetal Thymus	thymus
35	chr2:48643600-48644600	Weak transcription	Dnd41	blood
36	chr2:48643600-48644800	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr2:48643600-48645000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr2:48643600-48645000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr2:48643600-48645200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:48643600-48645400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr2:48643600-48645600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr2:48643600-48646600	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr2:48643600-48646800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr2:48643600-48646800	Weak transcription	HMEC	breast
45	chr2:48643600-48647000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr2:48643600-48647000	Weak transcription	Fetal Muscle Trunk	muscle
47	chr2:48643600-48647000	Weak transcription	Placenta	Placenta
48	chr2:48643600-48647000	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr2:48643600-48647000	Weak transcription	Right Atrium	heart
50	chr2:48643600-48647000	Weak transcription	Monocytes-CD14+_RO01746	blood

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