Variant report

Variant	rs41314542
Chromosome Location	chr1:213027042-213027043
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr1:213026747-213027599	A549	lung:	n/a	n/a
2	HNF4A	chr1:213026979-213027200	HepG2	liver:	n/a	n/a
3	SP1	chr1:213026773-213027569	A549	lung:	n/a	n/a
4	FOSL2	chr1:213026853-213027577	A549	lung:	n/a	n/a
5	REST	chr1:213026711-213027391	A549	lung:	n/a	n/a
6	FOXA2	chr1:213026933-213027573	A549	lung:	n/a	n/a
7	TEAD4	chr1:213026857-213027284	HepG2	liver:	n/a	n/a
8	EP300	chr1:213026891-213027521	A549	lung:	n/a	n/a
9	JUND	chr1:213026890-213027261	A549	lung:	n/a	n/a
10	MAX	chr1:213026716-213027559	A549	lung:	n/a	n/a
11	REST	chr1:213027002-213027226	H1-hESC	embryonic stem cell:	n/a	n/a
12	REST	chr1:213026825-213027268	A549	lung:	n/a	n/a
13	CEBPB	chr1:213026826-213027677	A549	lung:	n/a	n/a
14	EP300	chr1:213026776-213027521	A549	lung:	n/a	n/a
15	JUND	chr1:213027004-213027448	A549	lung:	n/a	chr1:213027300-213027311
16	GATA3	chr1:213026796-213027674	A549	lung:	n/a	n/a
17	MAFK	chr1:213026948-213027263	HepG2	liver:	n/a	chr1:213027133-213027148
18	BCL3	chr1:213026726-213027469	A549	lung:	n/a	n/a
19	FOSL2	chr1:213026761-213027416	A549	lung:	n/a	n/a
20	REST	chr1:213026989-213027169	K562	blood:	n/a	n/a
21	SIN3AK20	chr1:213027027-213027387	A549	lung:	n/a	n/a
22	CEBPB	chr1:213026879-213027123	HepG2	liver:	n/a	n/a
23	TCF12	chr1:213026810-213027685	A549	lung:	n/a	n/a
24	MAFF	chr1:213027026-213027271	HepG2	liver:	n/a	n/a
25	REST	chr1:213026871-213027252	HepG2	liver:	n/a	n/a
26	SP1	chr1:213026786-213027458	A549	lung:	n/a	n/a
27	RFX5	chr1:213026900-213027131	HepG2	liver:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:213025489..213028696-chr1:213029248..213033184,3	K562	blood:
2	chr1:213025871..213028763-chr1:213030169..213033277,3	MCF-7	breast:
3	chr1:213026064..213028809-chr1:213029690..213032627,2	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C1orf227-1	chr1:213025450-213027653	ENSG00000198468
2	lnc-C1orf227-1	chr1:213025450-213027651	ENSG00000198468.3

No data

Variant related genes	Relation type
FLVCR1	TF binding region
ENSG00000198468	Chromatin interaction
ENSG00000162769	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs2047288	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2047291	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2088256	1.00[AFR][1000 genomes]
rs3738799	1.00[AMR][1000 genomes]
rs3738801	1.00[AMR][1000 genomes]
rs3768549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41258005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41275386	1.00[AMR][1000 genomes]
rs41296666	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41296668	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41296674	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41296676	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41296678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41296680	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41297452	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41300027	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41300033	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41300035	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41300043	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41300979	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41301029	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs41307644	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41307646	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41314540	1.00[AMR][1000 genomes]
rs56300028	0.85[AMR][1000 genomes]
rs58746017	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73079880	0.85[AMR][1000 genomes]
rs73079886	0.85[AMR][1000 genomes]
rs73079887	0.85[AMR][1000 genomes]
rs7521050	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001637	chr1:212907611-213034606	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv508691	chr1:212998319-213028392	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
3	nsv1011186	chr1:213005165-213069563	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1013705	chr1:213005344-213064209	Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1008383	chr1:213025546-213114894	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213020400-213028600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:213022600-213030000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr1:213024200-213030000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:213024200-213030200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:213025200-213030200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr1:213025400-213029600	Weak transcription	Dnd41	blood
7	chr1:213025800-213027200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:213025800-213029800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:213025800-213030000	Weak transcription	Primary B cells from peripheral blood	blood
10	chr1:213026000-213030200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:213026000-213030200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr1:213026200-213027600	Enhancers	Fetal Intestine Small	intestine
13	chr1:213026200-213028400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:213026200-213028400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:213026200-213029600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr1:213026200-213030400	Weak transcription	Right Atrium	heart
17	chr1:213026200-213030800	Weak transcription	Thymus	Thymus
18	chr1:213026400-213028400	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr1:213026400-213029800	Weak transcription	Brain Hippocampus Middle	brain
20	chr1:213026400-213030200	Weak transcription	Primary T cells from cord blood	blood
21	chr1:213026400-213030400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:213026600-213027200	Enhancers	Fetal Intestine Large	intestine
23	chr1:213026600-213030000	Weak transcription	Primary B cells from cord blood	blood
24	chr1:213026600-213030000	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr1:213026600-213030000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr1:213026600-213030000	Weak transcription	Colon Smooth Muscle	Colon
27	chr1:213026600-213030200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:213026600-213030200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:213026600-213030200	Weak transcription	Fetal Kidney	kidney
30	chr1:213026600-213030200	Weak transcription	Fetal Muscle Leg	muscle
31	chr1:213026600-213030200	Weak transcription	Spleen	Spleen
32	chr1:213026600-213030200	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr1:213026600-213030200	Weak transcription	NHEK	skin
34	chr1:213026800-213027200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
35	chr1:213026800-213027200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
36	chr1:213026800-213027200	Enhancers	H9 Cell Line	embryonic stem cell
37	chr1:213026800-213027200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:213026800-213027200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
39	chr1:213026800-213027400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:213026800-213027400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
41	chr1:213026800-213027400	Strong transcription	Primary hematopoietic stem cells	blood
42	chr1:213026800-213027800	Flanking Active TSS	A549	lung
43	chr1:213026800-213030000	Enhancers	HepG2	liver
44	chr1:213026800-213030200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr1:213027000-213027200	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr1:213027000-213027200	Enhancers	Liver	Liver
47	chr1:213027000-213030000	Weak transcription	Duodenum Mucosa	Duodenum
48	chr1:213027000-213030200	Weak transcription	Lung	lung

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