Variant report

Variant	rs3844080
Chromosome Location	chr1:247306833-247306834
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:247303809..247306920-chr1:247310014..247313822,3	MCF-7	breast:
2	chr1:247265068..247267248-chr1:247305560..247307197,2	MCF-7	breast:
3	chr1:247304460..247307892-chr1:247308798..247311379,4	K562	blood:
4	chr1:247305865..247308781-chr1:247312082..247316125,4	K562	blood:
5	chr1:247305778..247307279-chr20:47900377..47902023,2	K562	blood:

Variant related genes	Relation type
ENSG00000196418	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1007457	0.90[CHB][hapmap]
rs10465609	0.95[ASN][1000 genomes]
rs10465619	0.95[ASN][1000 genomes]
rs10493861	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10754536	0.90[CHB][hapmap]
rs10754537	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10802466	0.90[CHB][hapmap]
rs10802471	0.97[ASN][1000 genomes]
rs10802472	0.83[AFR][1000 genomes]
rs10924907	0.90[CHB][hapmap]
rs10924919	0.90[CHB][hapmap]
rs10924924	0.82[ASN][1000 genomes]
rs10924927	0.95[ASN][1000 genomes]
rs10924928	0.95[ASN][1000 genomes]
rs11801681	0.81[ASN][1000 genomes]
rs12058648	0.82[ASN][1000 genomes]
rs12076177	0.95[ASN][1000 genomes]
rs12076273	0.95[ASN][1000 genomes]
rs12093759	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12119007	0.90[CHB][hapmap]
rs12120049	0.82[ASN][1000 genomes]
rs12127349	0.90[CHB][hapmap]
rs12131094	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12133112	0.95[ASN][1000 genomes]
rs12133296	0.90[CHB][hapmap]
rs12133763	0.90[CHB][hapmap]
rs12141126	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12141797	0.90[CHB][hapmap]
rs12141826	0.90[CHB][hapmap]
rs12144733	0.90[CHB][hapmap]
rs12144854	0.81[ASN][1000 genomes]
rs12751386	0.90[CHB][hapmap]
rs16846292	0.97[ASN][1000 genomes]
rs1874407	0.89[CHB][hapmap]
rs192432	0.89[CHB][hapmap]
rs2172795	0.90[CHB][hapmap]
rs2270616	0.90[CHB][hapmap]
rs2379192	0.90[CHB][hapmap]
rs2890101	0.88[CHB][hapmap]
rs2890103	0.90[CHB][hapmap]
rs2890104	0.90[CHB][hapmap]
rs2890339	0.95[ASN][1000 genomes]
rs3736325	0.90[CHB][hapmap]
rs3806269	0.90[CHB][hapmap]
rs3844079	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4105113	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4925692	0.90[CHB][hapmap]
rs4925701	0.82[ASN][1000 genomes]
rs4925702	0.81[ASN][1000 genomes]
rs4925703	0.82[ASN][1000 genomes]
rs4925704	0.81[ASN][1000 genomes]
rs4925711	0.84[ASN][1000 genomes]
rs4925715	0.84[ASN][1000 genomes]
rs6426209	0.90[CHB][hapmap]
rs6426218	0.90[CHB][hapmap]
rs6426220	0.80[CHB][hapmap];0.84[CHD][hapmap];0.83[MEX][hapmap]
rs6659254	0.93[ASN][1000 genomes]
rs6669242	0.90[CHB][hapmap]
rs6675536	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6680033	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6685921	0.89[CHB][hapmap]
rs6688822	0.97[ASN][1000 genomes]
rs6693464	0.90[CHB][hapmap]
rs6695894	0.90[CHB][hapmap]
rs6699898	0.90[CHB][hapmap]
rs6700358	0.94[ASN][1000 genomes]
rs6700824	0.84[ASN][1000 genomes]
rs7521596	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7528817	0.90[CHB][hapmap]
rs7531763	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549674	0.90[CHB][hapmap]
rs9793102	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9803828	0.95[ASN][1000 genomes]
rs9803983	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873424	chr1:246991094-247366380	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv535417	chr1:247094131-247409000	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
4	nsv1005639	chr1:247094161-247401380	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
5	nsv535418	chr1:247094161-247401380	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
6	nsv916236	chr1:247124353-247409065	Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
7	nsv948419	chr1:247130577-247400404	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
8	nsv1012616	chr1:247173851-247365588	Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
9	nsv535420	chr1:247173851-247365588	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
10	nsv1002438	chr1:247173851-247401380	ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
11	nsv999352	chr1:247180668-247307074	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv535421	chr1:247180668-247307074	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
13	nsv997687	chr1:247180668-247348847	Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
14	nsv535422	chr1:247180668-247348847	ZNF genes & repeats Genic enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
15	nsv427974	chr1:247184802-247352964	ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
16	esv3336179	chr1:247195262-247373269	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
17	nsv873428	chr1:247226986-247346189	Bivalent Enhancer Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
18	nsv833126	chr1:247273084-247476150	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	n/a
19	esv1830156	chr1:247278707-247319489	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
20	nsv873432	chr1:247278707-247334323	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
21	nsv873433	chr1:247278707-247360368	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a
22	nsv549567	chr1:247279802-247306833	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
23	nsv1005008	chr1:247285853-247339833	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a
24	nsv535423	chr1:247285853-247339833	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs3844080	ZNF124	cis	Whole Blood	GTEx
rs3844080	ZNF669	cis	parietal	SCAN
rs3844080	CRY2	trans	parietal	SCAN
rs3844080		cis	Lymphoblastoid	GTEx
rs3844080	ZNF124	cis	cerebellum	SCAN
rs3844080	Hs.421238	cis	multi-tissue	Pritchard
rs3844080	ZNF124	cis	parietal	SCAN
rs3844080	ZNF124	Cis_1M	lymphoblastoid	RTeQTL
rs3844080	ZNF669	cis	cerebellum	SCAN
rs3844080	ZNF124	cis	multi-tissue	Pritchard

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247295200-247307400	Weak transcription	Right Ventricle	heart
2	chr1:247301800-247333000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:247302000-247334200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:247302200-247309000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
5	chr1:247302400-247313200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:247302400-247313400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
7	chr1:247302800-247315200	ZNF genes & repeats	Dnd41	blood
8	chr1:247303000-247313400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:247303000-247315400	ZNF genes & repeats	Liver	Liver
10	chr1:247303200-247313600	ZNF genes & repeats	Fetal Brain Female	brain
11	chr1:247303400-247316600	Weak transcription	Fetal Heart	heart
12	chr1:247303400-247318600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:247303400-247324600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:247303600-247324600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
15	chr1:247303800-247313400	ZNF genes & repeats	Primary B cells from cord blood	blood
16	chr1:247304000-247308000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
17	chr1:247304200-247308400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:247304200-247324400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:247304400-247308400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr1:247304800-247308000	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
21	chr1:247304800-247309800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr1:247304800-247313000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr1:247305200-247313000	Weak transcription	HSMMtube	muscle
24	chr1:247305400-247307000	Weak transcription	Stomach Mucosa	stomach
25	chr1:247305400-247308600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:247305400-247320000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:247305600-247307200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:247305600-247307200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr1:247305600-247308600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr1:247305600-247318200	Weak transcription	HepG2	liver
31	chr1:247305800-247307000	Weak transcription	A549	lung
32	chr1:247305800-247307200	Weak transcription	Stomach Smooth Muscle	stomach
33	chr1:247306400-247307000	Weak transcription	HSMM	muscle
34	chr1:247306400-247308000	ZNF genes & repeats	Primary T cells from cord blood	blood
35	chr1:247306400-247313600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
36	chr1:247306600-247307000	ZNF genes & repeats	Aorta	Aorta
37	chr1:247306600-247307000	Weak transcription	Hela-S3	cervix
38	chr1:247306600-247307400	ZNF genes & repeats	Pancreas	Pancrea
39	chr1:247306600-247307600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
40	chr1:247306600-247307800	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:247306600-247307800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:247306600-247307800	ZNF genes & repeats	Adipose Nuclei	Adipose
43	chr1:247306600-247308800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:247306600-247313400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:247306600-247313400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
46	chr1:247306600-247324000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
47	chr1:247306600-247324200	ZNF genes & repeats	GM12878-XiMat	blood
48	chr1:247306800-247307000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
49	chr1:247306800-247307000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
50	chr1:247306800-247307200	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links