Variant report

Variant	rs72668171
Chromosome Location	chr4:90031848-90031849
allele	A/G
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	MAX	chr4:90031662-90033107	K562	blood:	n/a	chr4:90032609-90032618 chr4:90032634-90032644
2	SIN3AK20	chr4:90031811-90033148	MCF-7	breast:	n/a	n/a
3	GABPA	chr4:90031608-90032150	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr4:90031760-90031910	HCPEpiC	choroid plexus:	n/a	n/a
5	MXI1	chr4:90031599-90033231	GM12878	blood:	n/a	chr4:90031789-90031804
6	MAX	chr4:90031818-90033188	HepG2	liver:	n/a	chr4:90032609-90032618 chr4:90032634-90032644
7	BHLHE40	chr4:90031774-90033235	K562	blood:	n/a	chr4:90032093-90032109 chr4:90031987-90032003
8	MAX	chr4:90031702-90033805	A549	lung:	n/a	chr4:90032609-90032618 chr4:90032634-90032644
9	POLR2A	chr4:90031741-90033492	GM19099	blood:	n/a	n/a
10	E2F6	chr4:90031734-90033155	H1-hESC	embryonic stem cell:	n/a	chr4:90032663-90032672 chr4:90032574-90032586 chr4:90032633-90032642 chr4:90032628-90032638
11	POLR2A	chr4:90031758-90033089	MCF-7	breast:	n/a	n/a
12	E2F6	chr4:90031686-90033217	H1-hESC	embryonic stem cell:	n/a	chr4:90032663-90032672 chr4:90032574-90032586 chr4:90032633-90032642 chr4:90032628-90032638
13	CHD1	chr4:90031786-90033305	GM12878	blood:	n/a	n/a
14	MYC	chr4:90031682-90032925	A549	lung:	n/a	chr4:90032609-90032618 chr4:90032634-90032644
15	RCOR1	chr4:90031590-90032995	GM12878	blood:	n/a	n/a
16	MYC	chr4:90031728-90033645	K562	blood:	n/a	chr4:90032609-90032618 chr4:90032634-90032644
17	MXI1	chr4:90031723-90034038	HepG2	liver:	n/a	chr4:90031789-90031804
18	ARID3A	chr4:90031746-90032396	HepG2	liver:	n/a	n/a
19	USF2	chr4:90031770-90032744	GM12878	blood:	n/a	chr4:90032093-90032109 chr4:90031987-90032003
20	MXI1	chr4:90031727-90032024	H1-hESC	embryonic stem cell:	n/a	chr4:90031789-90031804
21	POLR2A	chr4:90031750-90033337	GM12878	blood:	n/a	n/a
22	MAX	chr4:90031663-90033047	H1-hESC	embryonic stem cell:	n/a	chr4:90032609-90032618 chr4:90032634-90032644
23	RCOR1	chr4:90031445-90033946	K562	blood:	n/a	n/a
24	WRNIP1	chr4:90031705-90033370	GM12878	blood:	n/a	n/a
25	JUND	chr4:90031790-90033679	K562	blood:	n/a	chr4:90033397-90033406
26	MAZ	chr4:90031500-90033296	K562	blood:	n/a	chr4:90032609-90032618 chr4:90032634-90032644
27	SIN3A	chr4:90031671-90033679	H1-hESC	embryonic stem cell:	n/a	chr4:90031994-90032003 chr4:90032056-90032070 chr4:90031990-90032004 chr4:90032616-90032627 chr4:90031996-90032004
28	REST	chr4:90031556-90033473	H1-neurons	neurons:	n/a	chr4:90031993-90032003 chr4:90032055-90032069 chr4:90032055-90032075 chr4:90031991-90032005 chr4:90032057-90032067 chr4:90032055-90032075 chr4:90032059-90032072 chr4:90031988-90032001 chr4:90032056-90032074
29	MAX	chr4:90031578-90033199	ECC-1	luminal epithelium:	n/a	chr4:90032609-90032618 chr4:90032634-90032644
30	TBP	chr4:90031679-90032139	H1-hESC	embryonic stem cell:	n/a	n/a
31	MAX	chr4:90031680-90033090	H1-hESC	embryonic stem cell:	n/a	chr4:90032609-90032618 chr4:90032634-90032644
32	MYC	chr4:90031577-90033521	K562	blood:	n/a	chr4:90032609-90032618 chr4:90032634-90032644
33	E2F6	chr4:90031775-90033218	A549	lung:	n/a	chr4:90032663-90032672 chr4:90032574-90032586 chr4:90032633-90032642 chr4:90032628-90032638
34	CTCF	chr4:90031634-90033263	SK-N-SH	brain:	n/a	n/a
35	MXI1	chr4:90030919-90033825	SK-N-SH	brain:	n/a	chr4:90031789-90031804
36	TCF12	chr4:90031725-90033905	A549	lung:	n/a	n/a
37	CHD2	chr4:90031842-90033118	GM12878	blood:	n/a	n/a
38	E2F6	chr4:90031737-90033048	K562	blood:	n/a	chr4:90032663-90032672 chr4:90032574-90032586 chr4:90032633-90032642 chr4:90032628-90032638
39	CTCF	chr4:90031311-90033365	A549	lung:	n/a	n/a
40	MAX	chr4:90031672-90031986	H1-hESC	embryonic stem cell:	n/a	n/a
41	BACH1	chr4:90031823-90032669	H1-hESC	embryonic stem cell:	n/a	n/a
42	SETDB1	chr4:90031327-90033996	U2OS	brain:	n/a	n/a
43	HCFC1	chr4:90031624-90033248	K562	blood:	n/a	n/a
44	MAX	chr4:90031805-90032823	HUVEC	blood vessel:	n/a	chr4:90032609-90032618 chr4:90032634-90032644
45	GABPA	chr4:90031608-90032246	MCF-7	breast:	n/a	n/a
46	POLR2A	chr4:90031640-90033194	H1-neurons	neurons:	n/a	n/a
47	MXI1	chr4:90031119-90033780	IMR90	lung:	n/a	chr4:90031789-90031804
48	MAX	chr4:90031748-90033179	K562	blood:	n/a	chr4:90032609-90032618 chr4:90032634-90032644
49	MAX	chr4:90031602-90033894	A549	lung:	n/a	chr4:90032609-90032618 chr4:90032634-90032644
50	RELA	chr4:90031722-90033075	GM18951	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:89739936..89740488-chr4:90031811..90032510,2	MCF-7	breast:
2	chr4:89443831..89446134-chr4:90031080..90033028,2	K562	blood:
3	chr4:89739661..89740284-chr4:90031824..90032453,2	MCF-7	breast:
4	chr4:89739934..89740458-chr4:90031072..90031943,2	K562	blood:
5	chr4:90021012..90023295-chr4:90030744..90032396,2	K562	blood:
6	chr4:90030188..90033002-chr4:90049823..90052502,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271359	TF binding region
TIGD2	TF binding region
ENSG00000138641	Chromatin interaction
ENSG00000145337	Chromatin interaction
ENSG00000212226	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10025332	0.83[ASN][1000 genomes]
rs10516826	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10516828	0.89[ASN][1000 genomes]
rs12507349	0.89[ASN][1000 genomes]
rs1398945	0.89[ASN][1000 genomes]
rs1513820	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17015025	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17768752	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17769356	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17770293	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17819929	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17820320	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17821105	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1921680	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2175821	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2280099	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2869974	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3822085	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5026462	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55806245	0.84[ASN][1000 genomes]
rs55885459	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55987745	0.87[ASN][1000 genomes]
rs55996516	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56038841	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56111951	0.89[ASN][1000 genomes]
rs56147277	0.84[ASN][1000 genomes]
rs56165603	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56344658	0.89[ASN][1000 genomes]
rs56355329	0.89[ASN][1000 genomes]
rs56672432	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56719325	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59188553	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59283403	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59586695	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60213126	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60591238	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60751124	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61082288	0.84[ASN][1000 genomes]
rs62306393	0.98[ASN][1000 genomes]
rs6822256	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6825767	0.83[ASN][1000 genomes]
rs6825804	0.83[ASN][1000 genomes]
rs6826703	0.81[ASN][1000 genomes]
rs6832298	0.84[ASN][1000 genomes]
rs72665855	0.81[ASN][1000 genomes]
rs72665867	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72665868	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72665882	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72665892	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72665898	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72665902	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72668111	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72668112	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72668120	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72668125	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72668127	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72668130	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72668134	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72668135	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72668138	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72668144	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72668152	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72668154	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72668156	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72668157	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72668165	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72668167	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72668179	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72668183	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72668187	0.89[ASN][1000 genomes]
rs72668189	0.87[ASN][1000 genomes]
rs72668192	0.84[ASN][1000 genomes]
rs72668193	0.84[ASN][1000 genomes]
rs72668195	0.83[ASN][1000 genomes]
rs72668196	0.83[ASN][1000 genomes]
rs72670003	0.83[ASN][1000 genomes]
rs756227	0.83[ASN][1000 genomes]
rs7660709	0.96[ASN][1000 genomes]
rs7669140	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7689498	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8582	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers 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 target site	10 gene(s)	inside rSNPs	diseases
4	nsv1002448	chr4:89933385-90128133	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv3437234	chr4:90031454-90034302	Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90030800-90033600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr4:90031000-90033400	Active TSS	Pancreas	Pancrea
3	chr4:90031200-90033000	Active TSS	Fetal Brain Female	brain
4	chr4:90031200-90033200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr4:90031200-90033400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
6	chr4:90031400-90032000	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr4:90031400-90032000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
8	chr4:90031400-90032000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr4:90031400-90032000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr4:90031400-90032000	Flanking Active TSS	Liver	Liver
11	chr4:90031400-90032000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr4:90031400-90032000	Flanking Bivalent TSS/Enh	Fetal Lung	lung
13	chr4:90031400-90032200	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
14	chr4:90031400-90032200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr4:90031400-90032200	Flanking Active TSS	Duodenum Mucosa	Duodenum
16	chr4:90031400-90032200	Flanking Active TSS	Rectal Smooth Muscle	rectum
17	chr4:90031400-90032200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr4:90031400-90032400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:90031400-90032400	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr4:90031400-90032400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
21	chr4:90031400-90033400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
22	chr4:90031400-90033400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
23	chr4:90031400-90033600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr4:90031600-90032000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:90031600-90032000	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr4:90031600-90032000	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
27	chr4:90031600-90032000	Flanking Active TSS	Primary T cells from cord blood	blood
28	chr4:90031600-90032000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
29	chr4:90031600-90032000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
30	chr4:90031600-90032000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr4:90031600-90032000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
32	chr4:90031600-90032000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr4:90031600-90032000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr4:90031600-90032000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr4:90031600-90032000	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
36	chr4:90031600-90032000	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr4:90031600-90032000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr4:90031600-90032000	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
39	chr4:90031600-90032000	Flanking Active TSS	Brain Anterior Caudate	brain
40	chr4:90031600-90032000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
41	chr4:90031600-90032000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr4:90031600-90032000	Flanking Active TSS	Colon Smooth Muscle	Colon
43	chr4:90031600-90032000	Flanking Active TSS	Ovary	ovary
44	chr4:90031600-90032000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
45	chr4:90031600-90032000	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
46	chr4:90031600-90032000	Flanking Bivalent TSS/Enh	A549	lung
47	chr4:90031600-90032000	Flanking Bivalent TSS/Enh	HSMM	muscle
48	chr4:90031600-90032000	Flanking Active TSS	K562	blood
49	chr4:90031600-90032000	Flanking Bivalent TSS/Enh	NH-A	brain
50	chr4:90031600-90032000	Flanking Bivalent TSS/Enh	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links