Variant report

Variant	rs2269985
Chromosome Location	chr7:99001625-99001626
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:99001493-99002554	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr7:99001403-99001918	GM12878	blood:	n/a	n/a
3	POLR2A	chr7:99001099-99003743	K562	blood:	n/a	n/a
4	POLR2A	chr7:99001474-99002813	A549	lung:	n/a	n/a
5	POLR2A	chr7:99001587-99001635	GM12878	blood:	n/a	n/a
6	POLR2A	chr7:99001278-99002035	K562	blood:	n/a	n/a
7	POLR2A	chr7:99001190-99002966	HL-60	blood:	n/a	n/a
8	POLR2A	chr7:99001140-99003122	GM12878	blood:	n/a	n/a
9	POLR2A	chr7:99001460-99001688	MCF-7	breast:	n/a	n/a
10	POLR2A	chr7:99001362-99001807	GM12891	blood:	n/a	n/a
11	POLR2A	chr7:99001353-99001724	A549	lung:	n/a	n/a
12	POLR2A	chr7:99001466-99001677	A549	lung:	n/a	n/a
13	POLR2A	chr7:99001241-99001696	K562	blood:	n/a	n/a
14	POLR2A	chr7:99001093-99002963	GM12892	blood:	n/a	n/a
15	POLR2A	chr7:99001243-99001753	K562	blood:	n/a	n/a
16	POLR2A	chr7:99001142-99003001	K562	blood:	n/a	n/a
17	POLR2A	chr7:99001308-99002543	GM12878	blood:	n/a	n/a
18	POLR2A	chr7:99001327-99002945	GM12891	blood:	n/a	n/a
19	POLR2A	chr7:99001352-99001776	GM12892	blood:	n/a	n/a
20	POLR2A	chr7:99001099-99002205	SK-N-MC	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr7:99000792..99002474-chr7:99063738..99066262,2	K562	blood:
2	chr7:98971053..98973782-chr7:99000134..99003212,3	MCF-7	breast:
3	chr7:98995708..98998425-chr7:98998981..99002328,3	MCF-7	breast:
4	chr7:99000152..99002046-chr7:99035155..99037970,2	MCF-7	breast:

No data

Variant related genes	Relation type
BUD31	TF binding region
ENSG00000106246	Chromatin interaction
ENSG00000160917	Chromatin interaction
ENSG00000248919	Chromatin interaction
ENSG00000130429	Chromatin interaction
ENSG00000241468	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1002172	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1004387	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs10155966	0.82[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs10225314	0.84[EUR][1000 genomes]
rs10236149	0.82[ASN][1000 genomes]
rs10243678	0.86[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs10255399	0.84[ASN][1000 genomes]
rs10258757	0.82[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs10270459	0.82[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs10270917	0.82[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs10464604	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11539770	1.00[EUR][1000 genomes]
rs11762273	0.82[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs13240600	0.83[JPT][hapmap]
rs17161652	1.00[CEU][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs17161677	1.00[CEU][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17161692	0.84[GIH][hapmap]
rs17161698	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17161766	0.92[EUR][1000 genomes]
rs17161768	1.00[EUR][1000 genomes]
rs17161769	1.00[EUR][1000 genomes]
rs17161771	0.84[EUR][1000 genomes]
rs17161772	0.84[EUR][1000 genomes]
rs17161774	0.92[EUR][1000 genomes]
rs1985453	0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2057905	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2057906	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2072181	0.86[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs2074652	0.83[JPT][hapmap];1.00[YRI][hapmap]
rs2107705	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2240385	1.00[CEU][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2301889	0.84[GIH][hapmap]
rs2404322	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28495024	0.84[ASN][1000 genomes]
rs3764815	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3800960	1.00[CEU][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs45492098	1.00[EUR][1000 genomes]
rs45540134	1.00[EUR][1000 genomes]
rs45622743	1.00[EUR][1000 genomes]
rs58222677	1.00[EUR][1000 genomes]
rs58249136	0.84[AFR][1000 genomes]
rs58421977	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59986060	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61159815	1.00[EUR][1000 genomes]
rs61337492	0.92[EUR][1000 genomes]
rs61402640	1.00[EUR][1000 genomes]
rs61543997	1.00[EUR][1000 genomes]
rs6943920	0.81[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs72494451	1.00[EUR][1000 genomes]
rs72494452	1.00[EUR][1000 genomes]
rs73709637	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73709641	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs940336	1.00[CEU][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3433144	chr7:98777878-99060209	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv831068	chr7:98819572-99006481	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv831069	chr7:98948128-99127584	Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:98979400-99001800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:98980400-99003800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr7:98985600-99003800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr7:98987000-99004200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:98990000-99002800	Strong transcription	GM12878-XiMat	blood
6	chr7:98991000-99002000	Strong transcription	NHEK	skin
7	chr7:98991000-99002600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr7:98991000-99002600	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr7:98991400-99001800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr7:98991400-99001800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr7:98991400-99001800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr7:98991400-99002400	Strong transcription	Esophagus	oesophagus
13	chr7:98991400-99002400	Weak transcription	Right Atrium	heart
14	chr7:98991400-99004200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr7:98991600-99001800	Strong transcription	NHLF	lung
16	chr7:98991600-99002000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr7:98991600-99002000	Strong transcription	Adipose Nuclei	Adipose
18	chr7:98991600-99002400	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr7:98991600-99002800	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr7:98991600-99003000	Strong transcription	Primary T cells from cord blood	blood
21	chr7:98991600-99003000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr7:98991600-99003400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr7:98991600-99003400	Weak transcription	Stomach Mucosa	stomach
24	chr7:98991600-99003400	Strong transcription	K562	blood
25	chr7:98991600-99005200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr7:98991800-99001800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr7:98991800-99002000	Strong transcription	Gastric	stomach
28	chr7:98991800-99002800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr7:98991800-99002800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr7:98991800-99003000	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr7:98991800-99003000	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr7:98991800-99003000	Strong transcription	Primary B cells from peripheral blood	blood
33	chr7:98991800-99003400	Strong transcription	Duodenum Mucosa	Duodenum
34	chr7:98991800-99003400	Strong transcription	Fetal Intestine Small	intestine
35	chr7:98991800-99003600	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr7:98991800-99003600	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr7:98991800-99003600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr7:98991800-99003800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr7:98992000-99002200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr7:98992000-99002400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr7:98992000-99002600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr7:98992000-99002800	Strong transcription	H9 Cell Line	embryonic stem cell
43	chr7:98992000-99002800	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr7:98992000-99002800	Strong transcription	Colonic Mucosa	Colon
45	chr7:98992000-99003000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr7:98992000-99003000	Strong transcription	Brain Substantia Nigra	brain
47	chr7:98992000-99003000	Strong transcription	Fetal Intestine Large	intestine
48	chr7:98992000-99003000	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr7:98992000-99003200	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr7:98992000-99003400	Strong transcription	Fetal Muscle Leg	muscle

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