Variant report

Variant	rs7998996
Chromosome Location	chr13:50086253-50086254
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50068733..50070336-chr13:50083872..50086385,2	MCF-7	breast:
2	chr13:50086064..50088335-chr13:50090580..50092913,2	K562	blood:
3	chr13:50085860..50087945-chr13:50089850..50091816,2	MCF-7	breast:
4	chr13:50072605..50075983-chr13:50085931..50088388,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136147	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12429621	0.88[TSI][hapmap]
rs17072932	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]
rs17072933	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17073175	0.88[TSI][hapmap]
rs55788913	1.00[EUR][1000 genomes]
rs60723161	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67216195	0.90[ASN][1000 genomes]
rs7318481	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[ASN][1000 genomes]
rs73188685	0.83[ASN][1000 genomes]
rs73188686	0.90[ASN][1000 genomes]
rs7324615	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7324805	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7358961	0.81[ASN][1000 genomes]
rs7990424	0.90[ASN][1000 genomes]
rs7994710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7998078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316456	1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs9591262	0.81[ASN][1000 genomes]
rs9591264	0.90[ASN][1000 genomes]
rs9591288	1.00[JPT][hapmap]
rs9596107	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9596108	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[ASN][1000 genomes]
rs9596110	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]
rs9596111	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9596112	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9596116	0.90[ASN][1000 genomes]
rs9596127	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047311	chr13:49895019-50224227	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv430561	chr13:49930643-50089844	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv430566	chr13:49945247-50089844	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv430570	chr13:49961137-50089844	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv523648	chr13:50005444-50086266	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv561613	chr13:50013622-50086266	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv900070	chr13:50013622-50087142	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv561614	chr13:50042983-50086253	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv561615	chr13:50042983-50086266	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
11	nsv1036135	chr13:50071310-50183103	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
12	nsv541770	chr13:50071310-50183103	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50070200-50089200	Weak transcription	Fetal Brain Male	brain
2	chr13:50070800-50086600	Weak transcription	Psoas Muscle	Psoas
3	chr13:50070800-50086800	Weak transcription	Ovary	ovary
4	chr13:50070800-50087400	Weak transcription	Placenta	Placenta
5	chr13:50070800-50087600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr13:50070800-50087800	Weak transcription	Aorta	Aorta
7	chr13:50070800-50087800	Weak transcription	NHEK	skin
8	chr13:50070800-50088000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr13:50070800-50088000	Weak transcription	Brain Anterior Caudate	brain
10	chr13:50070800-50088000	Weak transcription	Esophagus	oesophagus
11	chr13:50070800-50088000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr13:50070800-50088200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr13:50070800-50088200	Weak transcription	Brain Substantia Nigra	brain
14	chr13:50070800-50095600	Weak transcription	Fetal Kidney	kidney
15	chr13:50071000-50087800	Weak transcription	Colonic Mucosa	Colon
16	chr13:50071000-50087800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr13:50071000-50087800	Weak transcription	Right Ventricle	heart
18	chr13:50071000-50088000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr13:50071000-50093400	Weak transcription	HepG2	liver
20	chr13:50071400-50087000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr13:50071400-50087200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr13:50071800-50087200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr13:50071800-50088000	Weak transcription	Pancreas	Pancrea
24	chr13:50074000-50093000	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr13:50074800-50086400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr13:50075000-50086800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr13:50075000-50087000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr13:50075000-50087800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr13:50075000-50087800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr13:50075000-50088200	Weak transcription	HMEC	breast
31	chr13:50075000-50102400	Weak transcription	NH-A	brain
32	chr13:50075000-50143800	Weak transcription	Small Intestine	intestine
33	chr13:50075200-50087800	Weak transcription	Osteobl	bone
34	chr13:50075400-50088000	Weak transcription	Colon Smooth Muscle	Colon
35	chr13:50077400-50087800	Weak transcription	Left Ventricle	heart
36	chr13:50077600-50086600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr13:50077600-50086800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr13:50077600-50088000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr13:50077600-50088000	Weak transcription	Gastric	stomach
40	chr13:50077600-50088000	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr13:50077600-50088000	Weak transcription	Spleen	Spleen
42	chr13:50077600-50114000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr13:50078200-50086800	Weak transcription	Fetal Intestine Large	intestine
44	chr13:50078400-50086400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr13:50078400-50086600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr13:50078600-50086600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr13:50078600-50086800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr13:50078600-50088000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr13:50080000-50087400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr13:50080000-50087800	Weak transcription	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links