Variant report

Variant	rs13198600
Chromosome Location	chr6:15240441-15240442
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:15239185..15241876-chr6:15241948..15244748,3	MCF-7	breast:
2	chr6:15238350..15240596-chr6:15246578..15248795,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs13191127	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13197919	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs13203059	1.00[AFR][1000 genomes]
rs13203659	1.00[AFR][1000 genomes]
rs13203744	1.00[AFR][1000 genomes]
rs13206138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13206695	0.85[EUR][1000 genomes]
rs13209122	0.92[EUR][1000 genomes]
rs13209721	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13210652	0.84[EUR][1000 genomes]
rs13213534	0.85[EUR][1000 genomes]
rs13215638	0.85[EUR][1000 genomes]
rs13216551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13216625	0.85[EUR][1000 genomes]
rs13219748	0.92[EUR][1000 genomes]
rs34048058	0.84[EUR][1000 genomes]
rs34144528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34156913	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34229995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34340185	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs34390534	0.92[EUR][1000 genomes]
rs34470245	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34488826	1.00[EUR][1000 genomes]
rs34677259	0.92[EUR][1000 genomes]
rs34790337	0.84[EUR][1000 genomes]
rs34816087	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34816488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34934295	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35070076	1.00[AFR][1000 genomes]
rs35147300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35378362	0.92[EUR][1000 genomes]
rs35659244	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs35660009	0.85[EUR][1000 genomes]
rs35981238	0.92[EUR][1000 genomes]
rs67845400	0.85[EUR][1000 genomes]
rs71533639	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71533640	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71533642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71551024	1.00[AFR][1000 genomes]
rs71551025	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs71551028	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71551030	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71551032	0.92[EUR][1000 genomes]
rs71551033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71551034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71551035	0.89[EUR][1000 genomes]
rs71551040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71551041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71551042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71551043	0.96[EUR][1000 genomes]
rs71551045	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs71551046	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7740407	0.92[EUR][1000 genomes]
rs9383028	0.85[EUR][1000 genomes]
rs9476760	0.85[EUR][1000 genomes]
rs9476761	0.85[EUR][1000 genomes]
rs9476782	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9476783	0.92[EUR][1000 genomes]
rs9476784	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9476790	1.00[AMR][1000 genomes]
rs9476793	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9476794	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9476797	0.92[EUR][1000 genomes]
rs9476798	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830593	chr6:15049636-15244190	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv830594	chr6:15171158-15261296	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1027010	chr6:15201803-15425629	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1030558	chr6:15234675-15449137	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv538141	chr6:15234675-15509163	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15224400-15242000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:15238800-15240800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:15239200-15241000	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr6:15239400-15240800	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr6:15239600-15240600	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr6:15239600-15240600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:15239600-15240600	Enhancers	Adipose Nuclei	Adipose
8	chr6:15239600-15240600	Enhancers	Brain Germinal Matrix	brain
9	chr6:15239600-15240800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
10	chr6:15239600-15240800	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr6:15239600-15240800	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr6:15239600-15241000	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr6:15239600-15241000	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr6:15239800-15240600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr6:15239800-15240600	Enhancers	Duodenum Smooth Muscle	Duodenum
16	chr6:15240000-15240600	Enhancers	Rectal Mucosa Donor 29	rectum
17	chr6:15240000-15240600	Enhancers	HSMM	muscle
18	chr6:15240000-15243400	Weak transcription	Right Ventricle	heart
19	chr6:15240000-15244400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr6:15240000-15244600	Weak transcription	Left Ventricle	heart
21	chr6:15240000-15244600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr6:15240000-15244800	Weak transcription	Aorta	Aorta
23	chr6:15240000-15244800	Weak transcription	Right Atrium	heart
24	chr6:15240200-15240600	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr6:15240200-15240800	Enhancers	Fetal Heart	heart
26	chr6:15240200-15242200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr6:15240200-15243600	Weak transcription	Fetal Muscle Leg	muscle
28	chr6:15240200-15244600	Weak transcription	Colon Smooth Muscle	Colon
29	chr6:15240400-15241000	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr6:15240400-15241000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:15240400-15242400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr6:15240400-15242600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr6:15240400-15243000	Weak transcription	HUVEC	blood vessel
34	chr6:15240400-15244000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr6:15240400-15244200	Weak transcription	Rectal Smooth Muscle	rectum
36	chr6:15240400-15244200	Weak transcription	Stomach Smooth Muscle	stomach
37	chr6:15240400-15244400	Weak transcription	Fetal Brain Female	brain
38	chr6:15240400-15244400	Weak transcription	Fetal Lung	lung
39	chr6:15240400-15244400	Weak transcription	Fetal Stomach	stomach
40	chr6:15240400-15244400	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr6:15240400-15244600	Weak transcription	Brain Substantia Nigra	brain
42	chr6:15240400-15244600	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links