Variant report

Variant	rs4670642
Chromosome Location	chr2:37194704-37194705
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr2:37191247-37195519	SK-N-SH	brain:	n/a	chr2:37195144-37195159
2	TBP	chr2:37193595-37195208	HepG2	liver:	n/a	n/a
3	HDAC2	chr2:37194531-37195243	HepG2	liver:	n/a	n/a
4	FOXA2	chr2:37194642-37195270	HepG2	liver:	n/a	n/a
5	FOXA1	chr2:37194594-37195272	HepG2	liver:	n/a	n/a
6	MYC	chr2:37193534-37195540	K562	blood:	n/a	chr2:37195150-37195159
7	MAFK	chr2:37194202-37195143	K562	blood:	n/a	n/a
8	SMC3	chr2:37194697-37195095	HepG2	liver:	n/a	n/a
9	NFIC	chr2:37194492-37195257	HepG2	liver:	n/a	n/a
10	HA-E2F1	chr2:37193335-37194880	MCF-7	breast:	n/a	chr2:37193693-37193705 chr2:37194186-37194198
11	MYBL2	chr2:37194645-37195474	HepG2	liver:	n/a	n/a
12	SREBP1	chr2:37191874-37195394	GM12878	blood:	n/a	n/a
13	POLR2A	chr2:37193340-37195164	HepG2	liver:	n/a	n/a
14	CBX3	chr2:37194631-37196191	K562	blood:	n/a	n/a
15	NR2F2	chr2:37193301-37195153	K562	blood:	n/a	n/a
16	RCOR1	chr2:37193519-37195295	HepG2	liver:	n/a	n/a
17	IRF1	chr2:37193461-37196151	K562	blood:	n/a	chr2:37194295-37194305 chr2:37194295-37194309 chr2:37194524-37194541 chr2:37194522-37194542 chr2:37194291-37194305
18	RCOR1	chr2:37193089-37194717	K562	blood:	n/a	n/a
19	TEAD4	chr2:37194358-37195297	HepG2	liver:	n/a	n/a
20	SP1	chr2:37194550-37195329	HepG2	liver:	n/a	chr2:37195132-37195144 chr2:37195134-37195143
21	NFIC	chr2:37193878-37195443	HepG2	liver:	n/a	n/a
22	JUND	chr2:37193559-37194756	K562	blood:	n/a	chr2:37193974-37193983
23	REST	chr2:37193483-37194876	A549	lung:	n/a	chr2:37193679-37193692 chr2:37194197-37194210 chr2:37193626-37193639 chr2:37193622-37193632 chr2:37194093-37194106
24	MBD4	chr2:37193932-37195097	HepG2	liver:	n/a	n/a
25	FOXA1	chr2:37193574-37195488	HepG2	liver:	n/a	n/a
26	FOXA1	chr2:37194625-37195315	HepG2	liver:	n/a	n/a
27	HDAC2	chr2:37194662-37195345	HepG2	liver:	n/a	n/a
28	SIN3A	chr2:37192557-37195253	H1-hESC	embryonic stem cell:	n/a	chr2:37193961-37193972 chr2:37193626-37193639 chr2:37193638-37193649 chr2:37193927-37193938
29	POLR2A	chr2:37192869-37194859	PFSK-1	brain:	n/a	n/a
30	IRF1	chr2:37193470-37195353	K562	blood:	n/a	chr2:37194295-37194305 chr2:37194295-37194309 chr2:37194524-37194541 chr2:37194522-37194542 chr2:37194291-37194305
31	TBP	chr2:37193389-37195981	K562	blood:	n/a	n/a
32	EP300	chr2:37194581-37195306	HepG2	liver:	n/a	n/a
33	BHLHE40	chr2:37194689-37195186	HepG2	liver:	n/a	n/a
34	ARID3A	chr2:37194557-37195345	HepG2	liver:	n/a	n/a
35	POLR2A	chr2:37193340-37194828	MCF10A-Er-Src	breast:	n/a	n/a
36	FOXA2	chr2:37194382-37195528	HepG2	liver:	n/a	n/a
37	FOXA1	chr2:37194274-37195395	HepG2	liver:	n/a	n/a
38	TCF7L2	chr2:37194531-37195120	MCF-7	breast:	n/a	chr2:37194848-37194862
39	GATA1	chr2:37193387-37195305	PBDE	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:37194252..37196693-chr2:37198973..37200836,2	MCF-7	breast:
2	chr2:37194465..37196285-chr2:37212369..37214230,2	K562	blood:
3	chr2:37194557..37197275-chr2:37197696..37199511,3	K562	blood:
4	chr2:37193543..37195604-chr2:37419400..37421969,2	K562	blood:
5	chr2:37181946..37184586-chr2:37193992..37195533,2	K562	blood:
6	chr2:37194247..37196675-chr2:37203224..37205629,3	K562	blood:
7	chr2:37183661..37187179-chr2:37192061..37194972,3	MCF-7	breast:
8	chr2:37193659..37195188-chr2:37231958..37233613,2	MCF-7	breast:
9	chr2:37192443..37195662-chr2:37309226..37313144,4	K562	blood:
10	chr2:37194014..37195839-chr2:37202260..37204776,2	MCF-7	breast:

Variant related genes	Relation type
STRN	TF binding region
ENSG00000233159	Chromatin interaction
ENSG00000008869	Chromatin interaction
ENSG00000252518	Chromatin interaction
ENSG00000152133	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10190027	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11124556	0.81[ASN][1000 genomes]
rs11682782	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11684340	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11688446	0.82[AMR][1000 genomes]
rs11895180	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2110992	0.82[ASN][1000 genomes]
rs2372788	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2541007	0.81[ASN][1000 genomes]
rs3770770	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3770774	0.81[ASN][1000 genomes]
rs3796041	0.80[EUR][1000 genomes]
rs4670643	0.82[ASN][1000 genomes]
rs4670645	0.82[EUR][1000 genomes]
rs60572996	0.81[EUR][1000 genomes]
rs61380056	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62133071	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62133077	0.82[EUR][1000 genomes]
rs6709006	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6712162	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6723869	0.82[EUR][1000 genomes]
rs6728062	0.81[EUR][1000 genomes]
rs6739171	0.81[ASN][1000 genomes]
rs9636429	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]

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	nsv1004483	chr2:36875235-37356812	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv535644	chr2:36875235-37356812	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv428395	chr2:36990348-37300352	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv456363	chr2:37109281-37235324	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv581470	chr2:37109281-37235324	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
6	esv3440334	chr2:37192273-37194821	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	esv3344704	chr2:37192448-37195146	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37191800-37195000	Active TSS	NHDF-Ad	bronchial
2	chr2:37192000-37194800	Active TSS	Right Ventricle	heart
3	chr2:37192000-37195000	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr2:37192000-37195000	Active TSS	Psoas Muscle	Psoas
5	chr2:37192200-37194800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr2:37192200-37194800	Active TSS	H1 Cell Line	embryonic stem cell
7	chr2:37192200-37194800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:37192200-37194800	Active TSS	Rectal Smooth Muscle	rectum
9	chr2:37192200-37195000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:37192200-37195000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:37192400-37194800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:37192400-37194800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:37192400-37194800	Active TSS	Aorta	Aorta
14	chr2:37192400-37194800	Active TSS	Fetal Intestine Small	intestine
15	chr2:37192400-37194800	Active TSS	Fetal Kidney	kidney
16	chr2:37192600-37194800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr2:37192600-37194800	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr2:37192600-37194800	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr2:37192600-37194800	Active TSS	Stomach Smooth Muscle	stomach
20	chr2:37192600-37195000	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr2:37192800-37194800	Active TSS	Colon Smooth Muscle	Colon
22	chr2:37192800-37194800	Active TSS	Fetal Intestine Large	intestine
23	chr2:37192800-37194800	Active TSS	Stomach Mucosa	stomach
24	chr2:37193000-37194800	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr2:37193000-37194800	Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr2:37193200-37194800	Active TSS	Liver	Liver
27	chr2:37193800-37195200	Active TSS	Right Atrium	heart
28	chr2:37194000-37195000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:37194000-37195000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
30	chr2:37194000-37195400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr2:37194200-37194800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
32	chr2:37194200-37194800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
33	chr2:37194200-37194800	Flanking Active TSS	Primary T cells from cord blood	blood
34	chr2:37194200-37194800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr2:37194200-37194800	Flanking Active TSS	Brain Angular Gyrus	brain
36	chr2:37194200-37194800	Flanking Active TSS	Fetal Thymus	thymus
37	chr2:37194200-37194800	Flanking Active TSS	HUVEC	blood vessel
38	chr2:37194200-37195000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:37194200-37195000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr2:37194200-37195000	Flanking Active TSS	Osteobl	bone
41	chr2:37194200-37195200	Flanking Active TSS	Primary hematopoietic stem cells	blood
42	chr2:37194200-37195200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr2:37194200-37195200	Flanking Active TSS	Dnd41	blood
44	chr2:37194200-37195400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr2:37194400-37194800	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
46	chr2:37194400-37194800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
47	chr2:37194400-37194800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:37194400-37194800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
49	chr2:37194400-37194800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
50	chr2:37194400-37194800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links