Variant report

Variant	rs6918122
Chromosome Location	chr6:39188691-39188692
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:39187851..39189714-chr6:39273668..39275855,2	K562	blood:
2	chr6:39159091..39165465-chr6:39185781..39190794,6	K562	blood:
3	chr6:39173759..39176293-chr6:39187054..39189578,2	K562	blood:
4	chr6:39166640..39168889-chr6:39187099..39189518,2	MCF-7	breast:
5	chr6:39178389..39182010-chr6:39186397..39189185,3	MCF-7	breast:
6	chr6:39186927..39189268-chr6:39206677..39209448,2	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10807202	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947786	0.84[CHB][hapmap]
rs10947787	0.90[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10947788	0.92[CHB][hapmap];0.80[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs10947789	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12190363	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12200013	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12202900	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12207689	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2033226	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4711585	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4714223	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4714224	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs55818834	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72851851	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv830644	chr6:39116530-39325980	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1022974	chr6:39120271-39277553	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6918122	TDRG1	cis	cerebellum	SCAN
rs6918122	APOBEC2	cis	cerebellum	SCAN
rs6918122	PRICKLE4	cis	parietal	SCAN
rs6918122	LHFPL5	cis	parietal	SCAN
rs6918122	TREM2	cis	parietal	SCAN
rs6918122	PI16	cis	cerebellum	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39150600-39193800	Genic enhancers	Fetal Intestine Small	intestine
2	chr6:39156800-39193400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr6:39163800-39192800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:39169400-39193600	Enhancers	Liver	Liver
5	chr6:39174200-39195000	Enhancers	Stomach Mucosa	stomach
6	chr6:39178000-39193400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:39178600-39193200	Weak transcription	Thymus	Thymus
8	chr6:39181800-39189400	Genic enhancers	K562	blood
9	chr6:39182200-39190000	Enhancers	Pancreas	Pancrea
10	chr6:39182200-39195200	Enhancers	Fetal Lung	lung
11	chr6:39183200-39192800	Weak transcription	Right Atrium	heart
12	chr6:39183400-39192400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:39183600-39191000	Weak transcription	Esophagus	oesophagus
14	chr6:39184400-39191200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr6:39184400-39193400	Weak transcription	Hela-S3	cervix
16	chr6:39185000-39194400	Enhancers	Ovary	ovary
17	chr6:39185200-39188800	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr6:39185400-39189000	Enhancers	Spleen	Spleen
19	chr6:39185600-39192600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr6:39185800-39192000	Weak transcription	Adipose Nuclei	Adipose
21	chr6:39186000-39189600	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:39186000-39193800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr6:39186000-39193800	Genic enhancers	Fetal Intestine Large	intestine
24	chr6:39186200-39188800	Genic enhancers	H9 Cell Line	embryonic stem cell
25	chr6:39186200-39189000	Enhancers	Small Intestine	intestine
26	chr6:39186200-39190200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr6:39186200-39195000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr6:39186600-39189000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr6:39186800-39191000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr6:39187000-39191400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr6:39187000-39191600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr6:39187400-39189400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr6:39187400-39189400	Genic enhancers	Rectal Mucosa Donor 31	rectum
34	chr6:39187600-39190000	Genic enhancers	Duodenum Mucosa	Duodenum
35	chr6:39187600-39190800	Weak transcription	Primary hematopoietic stem cells	blood
36	chr6:39187600-39191200	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr6:39187600-39191600	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr6:39187600-39192200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:39187600-39193400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr6:39187800-39188800	Enhancers	Placenta	Placenta
41	chr6:39187800-39189000	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr6:39187800-39192000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr6:39187800-39192200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:39187800-39192400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr6:39188000-39189000	Weak transcription	Lung	lung
46	chr6:39188000-39189200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:39188000-39190400	Weak transcription	A549	lung
48	chr6:39188000-39190800	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr6:39188000-39191000	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr6:39188200-39188800	Enhancers	HUES48 Cell Line	embryonic stem cell

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