Variant report

Variant	rs7740398
Chromosome Location	chr6:46138405-46138406
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	POLR2A	chr6:46138239-46139054	MCF-7	breast:	n/a	n/a
2	CHD2	chr6:46138236-46139069	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr6:46138351-46139104	HCT-116	colon:	n/a	n/a
4	TAF1	chr6:46138237-46139121	ECC-1	luminal epithelium:	n/a	n/a
5	YY1	chr6:46138163-46138521	H1-hESC	embryonic stem cell:	n/a	chr6:46138343-46138355
6	TCF12	chr6:46138348-46139212	ECC-1	luminal epithelium:	n/a	n/a
7	EGR1	chr6:46138278-46139126	ECC-1	luminal epithelium:	n/a	chr6:46138522-46138535 chr6:46138726-46138736 chr6:46138338-46138347 chr6:46138523-46138534 chr6:46139116-46139126 chr6:46139111-46139124 chr6:46138523-46138532 chr6:46139115-46139125
8	TAF1	chr6:46138230-46139097	H1-hESC	embryonic stem cell:	n/a	n/a
9	MYC	chr6:46138353-46139043	MCF-7	breast:	n/a	n/a
10	ZEB1	chr6:46138382-46139004	GM12878	blood:	n/a	chr6:46138676-46138683 chr6:46138674-46138683
11	POLR2A	chr6:46138337-46138806	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr6:46137927-46139228	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr6:46138294-46139048	MCF-7	breast:	n/a	n/a
14	POLR2A	chr6:46138401-46139114	HCT-116	colon:	n/a	n/a
15	SP1	chr6:46138096-46139178	H1-hESC	embryonic stem cell:	n/a	chr6:46138726-46138735 chr6:46139114-46139126 chr6:46138867-46138881 chr6:46138526-46138536 chr6:46138888-46138897 chr6:46139115-46139129 chr6:46139121-46139133 chr6:46138721-46138730 chr6:46139115-46139125 chr6:46139122-46139132 chr6:46139116-46139125 chr6:46138101-46138110 chr6:46138726-46138740 chr6:46139121-46139133 chr6:46139115-46139124 chr6:46138725-46138737 chr6:46139114-46139126 chr6:46138732-46138753 chr6:46138871-46138880 chr6:46138721-46138730 chr6:46139122-46139131 chr6:46139122-46139136 chr6:46138725-46138737 chr6:46138870-46138882 chr6:46138722-46138731 chr6:46138727-46138736 chr6:46138097-46138111 chr6:46139123-46139132
16	TBP	chr6:46138283-46139133	H1-hESC	embryonic stem cell:	n/a	n/a
17	SIN3A	chr6:46138053-46139173	H1-hESC	embryonic stem cell:	n/a	chr6:46138842-46138851
18	CREB1	chr6:46138193-46139052	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr6:46138259-46139050	HCT-116	colon:	n/a	n/a
20	HA-E2F1	chr6:46138178-46138835	MCF-7	breast:	n/a	chr6:46138719-46138731 chr6:46138727-46138736 chr6:46138715-46138730
21	MAX	chr6:46138373-46139218	ECC-1	luminal epithelium:	n/a	n/a
22	GABPA	chr6:46138136-46139190	MCF-7	breast:	n/a	chr6:46139123-46139132 chr6:46139116-46139125
23	POLR2A	chr6:46138167-46139222	Raji	blood:	n/a	n/a
24	EGR1	chr6:46138314-46139138	ECC-1	luminal epithelium:	n/a	chr6:46139122-46139132 chr6:46139117-46139130 chr6:46138522-46138535 chr6:46138726-46138736 chr6:46138338-46138347 chr6:46138523-46138534 chr6:46139116-46139126 chr6:46139111-46139124 chr6:46138523-46138532 chr6:46139115-46139125
25	ZNF143	chr6:46138380-46138832	H1-hESC	embryonic stem cell:	n/a	chr6:46138718-46138736
26	MAX	chr6:46138369-46139158	H1-hESC	embryonic stem cell:	n/a	n/a
27	GABPA	chr6:46138026-46139182	MCF-7	breast:	n/a	chr6:46139123-46139132 chr6:46139116-46139125
28	ELF1	chr6:46138156-46139219	MCF-7	breast:	n/a	chr6:46139116-46139128 chr6:46138836-46138848
29	EGR1	chr6:46138203-46139222	HCT-116	colon:	n/a	chr6:46139122-46139132 chr6:46139117-46139130 chr6:46138522-46138535 chr6:46138726-46138736 chr6:46138338-46138347 chr6:46138523-46138534 chr6:46139116-46139126 chr6:46139111-46139124 chr6:46138523-46138532 chr6:46139115-46139125
30	POLR2A	chr6:46138195-46138432	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr6:46138179-46138835	H1-hESC	embryonic stem cell:	n/a	n/a
32	CHD1	chr6:46138293-46138638	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr6:46138383-46138916	H1-neurons	neurons:	n/a	n/a
34	EGR1	chr6:46138197-46139145	MCF-7	breast:	n/a	chr6:46139122-46139132 chr6:46139117-46139130 chr6:46138522-46138535 chr6:46138726-46138736 chr6:46138338-46138347 chr6:46138523-46138534 chr6:46139116-46139126 chr6:46139111-46139124 chr6:46138523-46138532 chr6:46139115-46139125
35	ZEB1	chr6:46138250-46138758	GM12878	blood:	n/a	chr6:46138676-46138683 chr6:46138674-46138683
36	USF1	chr6:46138361-46139150	ECC-1	luminal epithelium:	n/a	chr6:46138835-46138851 chr6:46138701-46138717
37	BRCA1	chr6:46138354-46138516	H1-hESC	embryonic stem cell:	n/a	n/a
38	TAF1	chr6:46138338-46138808	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr6:46138206-46139091	ECC-1	luminal epithelium:	n/a	n/a
40	CTCF	chr6:46138340-46138490	HEK293	kidney:	n/a	n/a
41	MAX	chr6:46138162-46139233	MCF-7	breast:	n/a	n/a
42	POLR2A	chr6:46138319-46139088	MCF-7	breast:	n/a	n/a
43	SIN3AK20	chr6:46138243-46139120	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr6:46138262-46139056	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr6:46138150-46139146	H1-hESC	embryonic stem cell:	n/a	n/a
46	MAX	chr6:46138245-46139197	H1-hESC	embryonic stem cell:	n/a	n/a
47	SP1	chr6:46138057-46139138	HCT-116	colon:	n/a	chr6:46138726-46138735 chr6:46139114-46139126 chr6:46138867-46138881 chr6:46138526-46138536 chr6:46138888-46138897 chr6:46139115-46139129 chr6:46139121-46139133 chr6:46138721-46138730 chr6:46139115-46139125 chr6:46139122-46139132 chr6:46139116-46139125 chr6:46138101-46138110 chr6:46138726-46138740 chr6:46139121-46139133 chr6:46139115-46139124 chr6:46138725-46138737 chr6:46139114-46139126 chr6:46138732-46138753 chr6:46138871-46138880 chr6:46138721-46138730 chr6:46139122-46139131 chr6:46139122-46139136 chr6:46138725-46138737 chr6:46138870-46138882 chr6:46138722-46138731 chr6:46138727-46138736 chr6:46138097-46138111 chr6:46139123-46139132
48	ZBTB7A	chr6:46138271-46138893	ECC-1	luminal epithelium:	n/a	n/a
49	POLR2A	chr6:46138401-46138847	HEK293	kidney:	n/a	n/a
50	EGR1	chr6:46138135-46139279	HCT-116	colon:	n/a	chr6:46139122-46139132 chr6:46139117-46139130 chr6:46138522-46138535 chr6:46138726-46138736 chr6:46138338-46138347 chr6:46138523-46138534 chr6:46139116-46139126 chr6:46139111-46139124 chr6:46138523-46138532 chr6:46139115-46139125

Variant related genes	Relation type
ENPP5	TF binding region

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1048076	1.00[YRI][hapmap]
rs1048079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1076736	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1076737	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10948280	0.93[EUR][1000 genomes]
rs11756160	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11758852	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12526912	0.83[AFR][1000 genomes]
rs12665453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs14781	1.00[YRI][hapmap]
rs2006030	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2022422	0.81[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2022423	0.83[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs2143746	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2179757	0.91[EUR][1000 genomes]
rs2206965	0.81[AFR][1000 genomes]
rs2206967	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2235881	0.81[AFR][1000 genomes]
rs2235883	0.81[AFR][1000 genomes]
rs2295016	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2295017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2295018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2894662	0.81[AFR][1000 genomes]
rs3756801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3806994	0.83[AFR][1000 genomes]
rs3806995	0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs3891763	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3905440	0.81[AFR][1000 genomes]
rs6458488	0.89[EUR][1000 genomes]
rs6458489	0.92[EUR][1000 genomes]
rs6458492	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6902187	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6921870	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6923745	0.81[AFR][1000 genomes]
rs6926570	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs6930766	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs6940977	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6941587	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7356841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7356846	0.94[CHB][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7745824	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7748442	0.81[AFR][1000 genomes]
rs7760123	0.92[EUR][1000 genomes]
rs7769738	1.00[YRI][hapmap]
rs7770384	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs9349345	0.88[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs9349348	0.81[AFR][1000 genomes]
rs9357501	0.81[AFR][1000 genomes]
rs9357502	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9367237	0.81[AFR][1000 genomes]
rs9369600	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs9369601	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9369602	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9381421	0.81[CEU][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes]
rs9381430	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs9395155	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9463184	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9472684	0.83[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs9472688	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9472689	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9472690	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9472692	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9472699	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9472705	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9472707	0.81[AFR][1000 genomes]
rs9472709	0.81[AFR][1000 genomes]
rs9472713	0.83[AFR][1000 genomes]
rs9472714	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9472715	0.83[AFR][1000 genomes]
rs9763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:46137400-46139200	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr6:46137400-46139400	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr6:46137600-46139200	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr6:46137600-46139200	Active TSS	Brain Angular Gyrus	brain
5	chr6:46137600-46139200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:46137800-46138600	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:46137800-46138600	Bivalent/Poised TSS	GM12878-XiMat	blood
8	chr6:46137800-46139000	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr6:46137800-46139000	Active TSS	Psoas Muscle	Psoas
10	chr6:46137800-46139200	Active TSS	H1 Cell Line	embryonic stem cell
11	chr6:46137800-46139200	Active TSS	Brain Substantia Nigra	brain
12	chr6:46137800-46139200	Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr6:46137800-46139400	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr6:46137800-46139400	Active TSS	H9 Cell Line	embryonic stem cell
15	chr6:46137800-46139400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:46137800-46139400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:46137800-46139400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:46137800-46139400	Active TSS	Fetal Brain Female	brain
19	chr6:46138000-46138600	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
20	chr6:46138000-46138600	Flanking Active TSS	Fetal Lung	lung
21	chr6:46138000-46138800	Flanking Bivalent TSS/Enh	Osteobl	bone
22	chr6:46138000-46139000	Bivalent/Poised TSS	Primary B cells from cord blood	blood
23	chr6:46138000-46139000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:46138000-46139000	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr6:46138000-46139000	Active TSS	Brain Germinal Matrix	brain
26	chr6:46138000-46139000	Active TSS	Fetal Intestine Large	intestine
27	chr6:46138000-46139000	Active TSS	Fetal Intestine Small	intestine
28	chr6:46138000-46139000	Active TSS	Lung	lung
29	chr6:46138000-46139000	Active TSS	Rectal Mucosa Donor 31	rectum
30	chr6:46138000-46139000	Bivalent/Poised TSS	NHLF	lung
31	chr6:46138000-46139200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr6:46138000-46139200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr6:46138000-46139200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr6:46138000-46139200	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr6:46138000-46139200	Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr6:46138000-46139200	Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr6:46138000-46139200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr6:46138000-46139200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr6:46138000-46139200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr6:46138000-46139200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:46138000-46139200	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr6:46138000-46139200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr6:46138000-46139200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
44	chr6:46138000-46139200	Active TSS	Colonic Mucosa	Colon
45	chr6:46138000-46139200	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr6:46138000-46139200	Active TSS	Ovary	ovary
47	chr6:46138000-46139200	Active TSS	Pancreas	Pancrea
48	chr6:46138000-46139200	Active TSS	Right Atrium	heart
49	chr6:46138000-46139200	Active TSS	HSMM	muscle
50	chr6:46138000-46139200	Active TSS	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links