Variant report

Variant	rs9498202
Chromosome Location	chr6:149383257-149383258
allele	G/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	NR3C1	chr6:149383159-149383426	A549	lung:	n/a	chr6:149383302-149383316 chr6:149383296-149383322 chr6:149383352-149383378 chr6:149383301-149383317 chr6:149383352-149383378 chr6:149383352-149383378 chr6:149383352-149383378
2	POLR2A	chr6:149381247-149384195	GM12878	blood:	n/a	n/a
3	FOXA1	chr6:149383084-149383503	A549	lung:	n/a	n/a
4	POLR2A	chr6:149381405-149383399	GM12878	blood:	n/a	n/a
5	POLR2A	chr6:149383057-149383397	GM12878	blood:	n/a	n/a
6	FOXA1	chr6:149383090-149383543	A549	lung:	n/a	n/a
7	NR3C1	chr6:149383098-149383401	A549	lung:	n/a	chr6:149383302-149383316 chr6:149383296-149383322 chr6:149383352-149383378 chr6:149383301-149383317 chr6:149383352-149383378 chr6:149383352-149383378 chr6:149383352-149383378
8	POLR2A	chr6:149381309-149383416	GM12878	blood:	n/a	n/a
9	NR3C1	chr6:149383093-149383459	A549	lung:	n/a	chr6:149383302-149383316 chr6:149383296-149383322 chr6:149383352-149383378 chr6:149383301-149383317 chr6:149383352-149383378 chr6:149383352-149383378 chr6:149383352-149383378
10	NR3C1	chr6:149383143-149383441	A549	lung:	n/a	chr6:149383302-149383316 chr6:149383296-149383322 chr6:149383352-149383378 chr6:149383301-149383317 chr6:149383352-149383378 chr6:149383352-149383378 chr6:149383352-149383378
11	NR3C1	chr6:149383078-149383518	A549	lung:	n/a	chr6:149383302-149383316 chr6:149383296-149383322 chr6:149383352-149383378 chr6:149383301-149383317 chr6:149383352-149383378 chr6:149383352-149383378 chr6:149383352-149383378
12	NR3C1	chr6:149383067-149383572	A549	lung:	n/a	chr6:149383302-149383316 chr6:149383296-149383322 chr6:149383352-149383378 chr6:149383301-149383317 chr6:149383352-149383378 chr6:149383352-149383378 chr6:149383352-149383378

No.	Distal block	Cell Line	Cell type
1	chr6:149356091..149358662-chr6:149380682..149383777,5	MCF-7	breast:
2	chr6:149381576..149384224-chr6:149749932..149753109,3	MCF-7	breast:
3	chr6:149347925..149355177-chr6:149378699..149385191,19	MCF-7	breast:
4	chr6:149367003..149368694-chr6:149381006..149384562,3	K562	blood:
5	chr6:149376456..149387248-chr6:149393069..149406749,44	MCF-7	breast:
6	chr6:149382098..149384824-chr6:149641581..149643098,2	MCF-7	breast:
7	chr6:149364981..149368017-chr6:149381154..149384452,3	MCF-7	breast:
8	chr6:149373800..149377779-chr6:149379783..149384195,7	MCF-7	breast:
9	chr6:149380862..149385743-chr6:149637114..149641554,7	MCF-7	breast:
10	chr6:149378324..149381149-chr6:149381718..149384310,2	K562	blood:

Variant related genes	Relation type
UST	TF binding region
ENSG00000236591	Chromatin interaction
ENSG00000055208	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10457075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10457839	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10457842	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10499251	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12153925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12196284	1.00[JPT][hapmap]
rs12197040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12200909	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12202158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12206419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1316376	0.84[EUR][1000 genomes]
rs13190879	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13217006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17669546	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1890610	1.00[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs1890612	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs1934221	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1934222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1934223	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1934227	0.84[CEU][hapmap]
rs2153251	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2153252	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2185250	1.00[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs34118116	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34599887	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3949414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4313020	1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4332004	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4336467	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4441968	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4454159	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs6570921	0.84[CEU][hapmap];0.82[GIH][hapmap]
rs6570923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6570924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6570926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6570927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6570932	1.00[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs6900527	1.00[JPT][hapmap]
rs6901626	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6902195	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6902487	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6909527	1.00[JPT][hapmap]
rs6909624	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6914281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6914318	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6914925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6917010	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6924503	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6930713	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6930963	0.84[CEU][hapmap]
rs6932773	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6940664	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6940915	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7762928	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7773409	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs7776204	1.00[JPT][hapmap]
rs9322165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9390652	0.84[CEU][hapmap];0.85[GIH][hapmap]
rs9485353	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9498197	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9498199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9498201	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9498204	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9498205	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9498207	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[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	nsv1032690	chr6:149206106-149398712	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1032319	chr6:149271433-149550525	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv538470	chr6:149271433-149550525	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv830842	chr6:149272321-149427340	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149354400-149400600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:149359200-149383600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr6:149362600-149385200	Weak transcription	Aorta	Aorta
4	chr6:149362800-149401400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:149363200-149394000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:149369000-149398800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:149371400-149396400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:149371800-149397000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:149375800-149384000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:149379200-149383400	Enhancers	Fetal Lung	lung
11	chr6:149379200-149385000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr6:149379400-149384200	Enhancers	Placenta	Placenta
13	chr6:149379400-149388600	Enhancers	Fetal Thymus	thymus
14	chr6:149380200-149384000	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr6:149380200-149386000	Enhancers	HSMMtube	muscle
16	chr6:149380400-149385800	Enhancers	HSMM	muscle
17	chr6:149380400-149386600	Enhancers	GM12878-XiMat	blood
18	chr6:149380800-149387400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr6:149380800-149388400	Enhancers	Fetal Stomach	stomach
20	chr6:149380800-149396200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr6:149381000-149385400	Flanking Active TSS	Dnd41	blood
22	chr6:149381000-149394800	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr6:149381000-149395000	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr6:149381200-149383800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:149381200-149385400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:149381400-149385400	Enhancers	Right Ventricle	heart
27	chr6:149381600-149383400	Flanking Active TSS	HepG2	liver
28	chr6:149381600-149385000	Enhancers	Right Atrium	heart
29	chr6:149381800-149383600	Enhancers	Stomach Mucosa	stomach
30	chr6:149381800-149384000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr6:149381800-149384000	Enhancers	Fetal Heart	heart
32	chr6:149381800-149384800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr6:149381800-149394600	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr6:149382000-149383400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr6:149382000-149383800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr6:149382000-149384000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr6:149382000-149384000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:149382000-149384200	Weak transcription	Brain Hippocampus Middle	brain
39	chr6:149382000-149387000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:149382200-149383600	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr6:149382200-149383800	Weak transcription	Psoas Muscle	Psoas
42	chr6:149382200-149384000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr6:149382200-149384200	Enhancers	Brain Substantia Nigra	brain
44	chr6:149382200-149400000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr6:149382400-149383600	Enhancers	Brain Anterior Caudate	brain
46	chr6:149382400-149383600	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr6:149382400-149383600	Enhancers	Pancreatic Islets	Pancreatic Islet
48	chr6:149382400-149383800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr6:149382400-149384400	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr6:149382400-149387000	Weak transcription	Primary B cells from cord blood	blood

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