Variant report

Variant	rs1200428
Chromosome Location	chr6:45518202-45518203
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:45389098..45392370-chr6:45517089..45519379,3	MCF-7	breast:
2	chr6:45512077..45515403-chr6:45517360..45519665,3	K562	blood:
3	chr6:45517438..45520580-chr6:45520902..45524408,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124813	Chromatin interaction
ENSG00000271857	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10214519	1.00[JPT][hapmap]
rs10485422	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10948237	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10948238	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11756145	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12195878	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12197948	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12204049	1.00[ASN][1000 genomes]
rs12209785	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs12210100	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12215249	0.85[ASN][1000 genomes]
rs1316330	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1317777	1.00[JPT][hapmap]
rs13201287	0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13207392	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs13208741	0.90[ASN][1000 genomes]
rs1928533	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1934327	1.00[JPT][hapmap]
rs1934329	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2031966	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2396442	1.00[JPT][hapmap]
rs2677110	1.00[JPT][hapmap]
rs2790098	1.00[JPT][hapmap]
rs2819864	1.00[JPT][hapmap]
rs2819866	1.00[JPT][hapmap]
rs4438954	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4714854	1.00[JPT][hapmap]
rs4714859	0.95[ASN][1000 genomes]
rs6458445	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6458446	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6458447	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6904353	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6905181	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6905847	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6911664	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6915569	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6932037	0.91[ASN][1000 genomes]
rs72864634	1.00[ASN][1000 genomes]
rs7748231	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7755257	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7756094	0.83[ASN][1000 genomes]
rs7760160	0.83[ASN][1000 genomes]
rs7772562	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9472494	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv427755	chr6:45474631-45627025	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv1019561	chr6:45485826-45535222	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv538214	chr6:45485826-45535222	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv491939	chr6:45508319-45526327	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1200428	ZNF318	cis	parietal	SCAN
rs1200428	KLHDC3	cis	cerebellum	SCAN
rs1200428	GTPBP2	cis	cerebellum	SCAN
rs1200428	MRPL2	cis	cerebellum	SCAN
rs1200428	C6orf141	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45465000-45521600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr6:45489000-45521800	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr6:45506800-45523400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr6:45507400-45518800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:45508200-45521600	Weak transcription	Primary T cells from cord blood	blood
6	chr6:45508200-45530600	Weak transcription	Psoas Muscle	Psoas
7	chr6:45508600-45522400	Weak transcription	Fetal Thymus	thymus
8	chr6:45508800-45523400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr6:45512000-45524000	Weak transcription	NHEK	skin
10	chr6:45512400-45523400	Weak transcription	Brain Substantia Nigra	brain
11	chr6:45512400-45523400	Weak transcription	HMEC	breast
12	chr6:45512600-45519400	Weak transcription	Fetal Stomach	stomach
13	chr6:45512600-45521600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:45512800-45520200	Weak transcription	Ovary	ovary
15	chr6:45515000-45521600	Weak transcription	Gastric	stomach
16	chr6:45515400-45518400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:45515400-45522400	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr6:45515400-45523400	Weak transcription	HSMMtube	muscle
19	chr6:45515600-45520600	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr6:45515600-45521200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr6:45515600-45521600	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr6:45515600-45521600	Weak transcription	Esophagus	oesophagus
23	chr6:45515600-45521800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:45515600-45521800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr6:45515800-45518800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr6:45515800-45522600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr6:45516000-45519800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr6:45516000-45521800	Weak transcription	NH-A	brain
29	chr6:45516800-45521400	Weak transcription	HSMM	muscle
30	chr6:45517000-45521600	Weak transcription	NHDF-Ad	bronchial
31	chr6:45517000-45521600	Weak transcription	NHLF	lung
32	chr6:45517000-45521800	Weak transcription	Dnd41	blood
33	chr6:45517000-45526000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr6:45517200-45518800	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr6:45517200-45520000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:45517200-45521600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr6:45517200-45521600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr6:45517200-45521600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr6:45517200-45521600	Weak transcription	Lung	lung
40	chr6:45517200-45521800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:45517200-45522000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr6:45517200-45522400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr6:45517200-45524600	Weak transcription	Placenta	Placenta
44	chr6:45517200-45524600	Weak transcription	Spleen	Spleen
45	chr6:45517400-45521600	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr6:45517400-45521600	Weak transcription	Osteobl	bone
47	chr6:45517400-45521800	Weak transcription	Hela-S3	cervix
48	chr6:45517400-45523400	Weak transcription	Duodenum Mucosa	Duodenum
49	chr6:45517800-45521200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr6:45518000-45521600	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links