Variant report

Variant	rs2138087
Chromosome Location	chr7:98625998-98625999
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:98625288-98626655	K562	blood:	n/a	n/a
2	POLR2A	chr7:98625943-98626155	GM12878	blood:	n/a	n/a
3	POLR2A	chr7:98625898-98626118	ProgFib	skin:	n/a	n/a
4	POLR2A	chr7:98625990-98626426	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr7:98625881-98626109	K562	blood:	n/a	n/a
6	POLR2A	chr7:98625731-98626024	HepG2	liver:	n/a	n/a
7	POLR2A	chr7:98625766-98626499	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr7:98625261-98627180	K562	blood:	n/a	n/a
9	POLR2A	chr7:98625853-98626401	MCF-7	breast:	n/a	n/a
10	POLR2A	chr7:98624837-98629944	K562	blood:	n/a	n/a
11	POLR2A	chr7:98625986-98626153	SK-N-SH	brain:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:98625983-98626033	BJ	skin:	n/a
2	chr7:98625983-98626033	Hela-S3	cervix:	n/a
3	chr7:98625983-98626033	NHDF-neo	bronchial:	n/a
4	chr7:98625983-98626033	AoSMC	blood vessel:	n/a
5	chr7:98625983-98626033	HRE	kidney:	n/a
6	chr7:98625983-98626033	K562	blood:	n/a
7	chr7:98625983-98626033	PANC-1	pancreas:	n/a
8	chr7:98625983-98626033	ovcar-3	ovarian:	n/a
9	chr7:98625983-98626033	H1-hESC	embryonic stem cell:	embryo
10	chr7:98625983-98626033	AG10803	skin:	n/a
11	chr7:98625983-98626033	GM12892	blood:	n/a
12	chr7:98625983-98626033	HMEC	breast:	n/a
13	chr7:98625983-98626033	HepG2	liver:	n/a
14	chr7:98625983-98626033	AG09309	skin:	n/a
15	chr7:98625983-98626033	GM12878	blood:	n/a
16	chr7:98625983-98626033	NB4	blood:	n/a
17	chr7:98625983-98626033	HPAEpiC	pulmonary alveolar:	n/a
18	chr7:98625983-98626033	SK-N-SH_RA	brain:	n/a
19	chr7:98625983-98626033	HCF	heart:	n/a
20	chr7:98625983-98626033	SKMC	muscle:	n/a
21	chr7:98625983-98626033	BE2_C	brain:	n/a
22	chr7:98625983-98626033	HCT-116	colon:	n/a
23	chr7:98625983-98626033	HCPEpiC	choroid plexus:	n/a
24	chr7:98625983-98626033	ECC-1	luminal epithelium:	n/a
25	chr7:98625983-98626033	HCM	heart:	n/a
26	chr7:98625983-98626033	GM06990	blood:	n/a
27	chr7:98625983-98626033	HEEpiC	esophagus:	n/a
28	chr7:98625983-98626033	Jurkat	blood:	n/a
29	chr7:98625983-98626033	MCF10A-Er-Src	breast:	n/a
30	chr7:98625983-98626033	HAEpiC	amniotic membrane:	n/a
31	chr7:98625983-98626033	SAEC	small airway:	n/a
32	chr7:98625983-98626033	HEK293	kidney:	embryo
33	chr7:98625983-98626033	GM12891	blood:	n/a
34	chr7:98625983-98626033	NT2-D1	testis:	n/a
35	chr7:98625983-98626033	AG04450	lung:	fetal
36	chr7:98625983-98626033	HRPEpiC	eye:	n/a
37	chr7:98625983-98626033	SK-N-MC	brain:	n/a
38	chr7:98625983-98626033	Hepatocyte	liver:	n/a
39	chr7:98625983-98626033	MCF-7	breast:	n/a
40	chr7:98625983-98626033	HRCEpiC	kidney:	n/a
41	chr7:98625983-98626033	PrEC	prostate:	n/a
42	chr7:98625983-98626033	U87	brain:	n/a
43	chr7:98625983-98626033	AG04449	skin:	fetal
44	chr7:98625983-98626033	T-47D	breast:	n/a
45	chr7:98625983-98626033	HIPEpiC	eye:	n/a
46	chr7:98625983-98626033	AG09319	gingival:	n/a
47	chr7:98625983-98626033	CMK	blood:	n/a
48	chr7:98625983-98626033	HNPCEpiC	eye:	n/a
49	chr7:98625983-98626033	RPTEC	kidney:	n/a
50	chr7:98625983-98626033	Caco-2	colon:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:98625520..98627401-chr7:98629881..98632572,3	K562	blood:
2	chr7:98625520..98627401-chr7:98629881..98632572,2	K562	blood:
3	chr7:98625274..98628239-chr7:98630668..98632654,2	MCF-7	breast:
4	chr7:98624718..98626899-chr7:98970267..98973066,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000242687	TF binding region
ENSG00000242687	CpG island
ENSG00000242687	Chromatin interaction
ENSG00000130429	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10231389	1.00[MEX][hapmap]
rs10235956	1.00[ASW][hapmap];0.93[LWK][hapmap];0.80[MKK][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10267068	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10275844	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10279813	0.86[AMR][1000 genomes]
rs10280276	1.00[MEX][hapmap]
rs11768515	0.86[AMR][1000 genomes]
rs11977121	1.00[EUR][1000 genomes]
rs160388	0.86[AMR][1000 genomes]
rs160391	0.86[AMR][1000 genomes]
rs1709724	0.81[AMR][1000 genomes]
rs1709725	0.81[AMR][1000 genomes]
rs1709727	0.81[AMR][1000 genomes]
rs17161567	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs219794	0.93[AMR][1000 genomes]
rs219801	0.83[ASW][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes]
rs219809	0.93[AMR][1000 genomes]
rs28502461	1.00[EUR][1000 genomes]
rs28525333	1.00[EUR][1000 genomes]
rs28556608	1.00[EUR][1000 genomes]
rs310742	0.81[AMR][1000 genomes]
rs310744	0.81[AMR][1000 genomes]
rs4413705	0.93[AMR][1000 genomes]
rs58666420	1.00[EUR][1000 genomes]
rs6949335	1.00[EUR][1000 genomes]
rs6963517	1.00[EUR][1000 genomes]
rs6979768	1.00[MEX][hapmap]
rs73395129	0.86[AMR][1000 genomes]
rs73404949	1.00[EUR][1000 genomes]
rs73407182	1.00[EUR][1000 genomes]
rs7788342	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024529	chr7:98194830-98793518	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv539036	chr7:98194830-98793518	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv1847495	chr7:98556216-98648069	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv1034506	chr7:98556216-98678440	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	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	chr7:98583800-98648800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:98604200-98627000	Weak transcription	Fetal Heart	heart
3	chr7:98604800-98627000	Weak transcription	Fetal Brain Male	brain
4	chr7:98607200-98629200	Weak transcription	Psoas Muscle	Psoas
5	chr7:98612000-98627800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr7:98612400-98627800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr7:98612400-98632000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr7:98612600-98627000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr7:98612800-98626400	Weak transcription	Brain Angular Gyrus	brain
10	chr7:98613400-98626000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr7:98613400-98629400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr7:98613600-98626600	Weak transcription	Fetal Kidney	kidney
13	chr7:98618200-98626000	Weak transcription	HMEC	breast
14	chr7:98618200-98626400	Weak transcription	Hela-S3	cervix
15	chr7:98618200-98626600	Weak transcription	K562	blood
16	chr7:98618200-98626800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr7:98618400-98626200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr7:98618600-98626000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr7:98618800-98628600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr7:98619800-98626600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr7:98620000-98626600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr7:98622600-98626800	Weak transcription	Stomach Mucosa	stomach
23	chr7:98622800-98626200	Weak transcription	NHDF-Ad	bronchial
24	chr7:98623400-98627000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr7:98623400-98640200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr7:98624600-98637200	Strong transcription	Fetal Intestine Large	intestine
27	chr7:98624800-98626800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr7:98624800-98627000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr7:98624800-98627000	Strong transcription	Skeletal Muscle Male	skeletal muscle
30	chr7:98624800-98627000	Genic enhancers	HUVEC	blood vessel
31	chr7:98624800-98627200	Strong transcription	Fetal Brain Female	brain
32	chr7:98624800-98627200	Strong transcription	Stomach Smooth Muscle	stomach
33	chr7:98624800-98627600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr7:98624800-98627600	Strong transcription	A549	lung
35	chr7:98624800-98627800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr7:98624800-98627800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr7:98624800-98627800	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr7:98624800-98633400	Strong transcription	Brain Substantia Nigra	brain
39	chr7:98624800-98637200	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr7:98624800-98644200	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr7:98624800-98651200	Strong transcription	Primary hematopoietic stem cells	blood
42	chr7:98624800-98653000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr7:98624800-98655200	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr7:98624800-98656600	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr7:98624800-98656600	Strong transcription	Dnd41	blood
46	chr7:98624800-98657800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr7:98624800-98658400	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr7:98625000-98626400	Strong transcription	Fetal Muscle Leg	muscle
49	chr7:98625000-98627000	Strong transcription	Fetal Lung	lung
50	chr7:98625000-98627000	Strong transcription	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links