Variant report

Variant	rs6674384
Chromosome Location	chr1:114455907-114455908
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:114300624..114304255-chr1:114455595..114460440,4	K562	blood:
2	chr1:114455126..114458709-chr1:114488876..114491433,3	K562	blood:
3	chr1:114453526..114463040-chr1:114468902..114474133,15	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HIPK1-1	chr1:114455538-114456662	NONHSAT005344

Variant related genes	Relation type
ENSG00000116793	Chromatin interaction
ENSG00000163349	Chromatin interaction
ENSG00000235527	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10108	0.94[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap]
rs10494162	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10494163	0.88[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap]
rs11102703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11102706	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11102707	0.97[CHD][hapmap];1.00[JPT][hapmap]
rs11102708	0.81[ASN][1000 genomes]
rs11102709	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12060750	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12125546	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12127377	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.87[ASN][1000 genomes]
rs12129050	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.81[ASN][1000 genomes]
rs1217444	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1503832	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1553449	0.89[ASN][1000 genomes]
rs1553450	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.87[ASN][1000 genomes]
rs17852555	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.82[ASN][1000 genomes]
rs1910485	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1985435	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1985436	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41302825	0.82[ASN][1000 genomes]
rs6537800	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6669370	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.82[ASN][1000 genomes]
rs7364	0.88[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs7519860	0.89[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7545300	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7546851	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs756493	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs878129	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv1826178	chr1:114331645-114471583	Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	esv1842398	chr1:114331645-114471583	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv1848035	chr1:114331645-114471583	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6674384	DCLRE1B	cis	lymphoblastoid	seeQTL
rs6674384	PTPN22	cis	parietal	SCAN
rs6674384	DCLRE1B	cis	multi-tissue	Pritchard
rs6674384	DENND2C	cis	cerebellum	SCAN
rs6674384	DCLRE1B	Cis_1M	lymphoblastoid	RTeQTL
rs6674384	DCLRE1B	cis	normal skin	skin_eQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114448600-114456000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:114448600-114456600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr1:114448600-114461400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr1:114448800-114456000	Weak transcription	Fetal Kidney	kidney
5	chr1:114449200-114461800	Weak transcription	Fetal Brain Male	brain
6	chr1:114449400-114456000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:114449600-114456800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:114449600-114458000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:114449800-114456600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:114449800-114457200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:114449800-114457200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:114449800-114470400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr1:114450000-114456000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:114450000-114456200	Strong transcription	Fetal Thymus	thymus
15	chr1:114450400-114456200	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr1:114450400-114456200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:114450400-114456200	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr1:114450600-114456200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr1:114450600-114456400	Strong transcription	Hela-S3	cervix
20	chr1:114451400-114456200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr1:114453000-114456000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr1:114453000-114456000	Strong transcription	Spleen	Spleen
23	chr1:114453200-114456000	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr1:114453600-114456200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:114453800-114456200	Strong transcription	HepG2	liver
26	chr1:114454200-114458200	Weak transcription	HUVEC	blood vessel
27	chr1:114454200-114459000	Weak transcription	Esophagus	oesophagus
28	chr1:114454400-114456400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr1:114454400-114458200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr1:114454600-114456200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:114454600-114456400	Genic enhancers	K562	blood
32	chr1:114454600-114461000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:114454800-114456600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:114454800-114456800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:114454800-114457000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr1:114454800-114457000	Weak transcription	Liver	Liver
37	chr1:114454800-114457600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr1:114454800-114457600	Weak transcription	GM12878-XiMat	blood
39	chr1:114455000-114456000	Enhancers	Small Intestine	intestine
40	chr1:114455000-114456200	Enhancers	Brain Hippocampus Middle	brain
41	chr1:114455000-114456800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr1:114455000-114457000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr1:114455000-114457200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:114455000-114457200	Enhancers	Fetal Heart	heart
45	chr1:114455000-114458800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:114455000-114459800	Weak transcription	HMEC	breast
47	chr1:114455000-114460000	Weak transcription	NHEK	skin
48	chr1:114455200-114456000	Enhancers	Fetal Lung	lung
49	chr1:114455200-114456200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:114455200-114456200	Enhancers	Colon Smooth Muscle	Colon

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