Variant report

Variant	rs6502557
Chromosome Location	chr17:16960978-16960979
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:16945357..16947606-chr17:16959220..16962216,2	K562	blood:
2	chr17:16960541..16963488-chr17:16973669..16975731,3	MCF-7	breast:
3	chr17:16959720..16962081-chr17:16964608..16966842,2	K562	blood:
4	chr17:16944990..16949876-chr17:16959315..16962454,4	MCF-7	breast:
5	chr17:16958422..16961495-chr17:16962516..16966035,3	MCF-7	breast:
6	chr17:16953800..16956981-chr17:16958258..16961708,4	MCF-7	breast:
7	chr17:16958465..16960222-chr17:16960878..16963338,2	K562	blood:

Variant related genes	Relation type
ENSG00000133030	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11868908	0.93[YRI][hapmap]
rs11869423	0.93[YRI][hapmap]
rs12601193	1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs12601424	0.92[ASN][1000 genomes]
rs12601453	1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs12602196	1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs12602675	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs16961340	0.92[ASN][1000 genomes]
rs16961396	1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs2271521	0.88[ASN][1000 genomes]
rs2292528	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs3744126	1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs3744135	1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs3744142	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs3803762	1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs3826304	0.82[ASN][1000 genomes]
rs4078534	1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs41319048	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs4316813	0.83[JPT][hapmap]
rs6502556	0.93[YRI][hapmap]
rs6502558	0.93[YRI][hapmap]
rs6502559	0.93[YRI][hapmap]
rs6502560	1.00[YRI][hapmap]
rs7220492	0.93[YRI][hapmap]
rs7223773	0.93[YRI][hapmap]
rs8064771	0.83[JPT][hapmap]
rs8066280	0.93[YRI][hapmap]
rs8067672	0.93[YRI][hapmap]
rs8068587	0.93[YRI][hapmap]
rs8069241	0.92[ASN][1000 genomes]
rs9908728	0.82[ASN][1000 genomes]
rs9909107	0.82[ASN][1000 genomes]

Variant related diseases (count:1)

Disease	PMID	Source
IgG glycosylation	23382691	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6502557	NT5M	cis	Whole Blood	GTEx
rs6502557	FLCN	cis	lymphoblastoid	seeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16949000-16962000	Enhancers	Fetal Heart	heart
2	chr17:16949000-16966200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr17:16949000-16975200	Weak transcription	K562	blood
4	chr17:16950200-16962600	Weak transcription	Dnd41	blood
5	chr17:16950200-16968200	Enhancers	Psoas Muscle	Psoas
6	chr17:16952600-16996400	Weak transcription	Fetal Brain Male	brain
7	chr17:16953600-16967600	Genic enhancers	Fetal Muscle Trunk	muscle
8	chr17:16953800-16961000	Enhancers	Right Atrium	heart
9	chr17:16953800-16961800	Genic enhancers	A549	lung
10	chr17:16954200-16961000	Enhancers	Stomach Mucosa	stomach
11	chr17:16954200-16962200	Genic enhancers	Fetal Stomach	stomach
12	chr17:16954800-16981200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr17:16955400-16970200	Weak transcription	NH-A	brain
14	chr17:16955400-16981200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr17:16956400-16972600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr17:16956600-16961400	Weak transcription	GM12878-XiMat	blood
17	chr17:16956600-16965600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr17:16956600-16966200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr17:16956800-16966000	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr17:16957000-16962400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr17:16957200-16962800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr17:16957200-16964800	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr17:16957200-16965800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr17:16957400-16963200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr17:16957400-16965000	Weak transcription	Primary B cells from cord blood	blood
26	chr17:16957600-16962200	Enhancers	Colon Smooth Muscle	Colon
27	chr17:16957600-16964000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr17:16957800-16963800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr17:16958200-16961000	Enhancers	HSMMtube	muscle
30	chr17:16958400-16961000	Enhancers	Brain Substantia Nigra	brain
31	chr17:16958600-16961000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr17:16958600-16961000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr17:16958800-16961600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr17:16958800-16965200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr17:16959200-16964600	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr17:16959200-16965400	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr17:16959200-16966800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr17:16959200-16982200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr17:16959400-16972800	Weak transcription	HUVEC	blood vessel
40	chr17:16959600-16961000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr17:16959600-16961400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr17:16959600-16961400	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr17:16959600-16963800	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr17:16959600-16966800	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr17:16959600-16966800	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr17:16959600-16979800	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr17:16959600-16992000	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr17:16959800-16963200	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr17:16959800-16964400	Strong transcription	Fetal Intestine Small	intestine
50	chr17:16959800-16966400	Weak transcription	Small Intestine	intestine

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