Variant report

Variant	rs2690116
Chromosome Location	chr6:25318499-25318500
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:25314690..25316229-chr6:25317879..25319908,2	K562	blood:
2	chr6:25304384..25306204-chr6:25317255..25319611,2	MCF-7	breast:
3	chr6:25316945..25319715-chr6:25323364..25325803,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CMAHP-5	chr6:25318493-25318508	NONHSAT108153

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1815097	1.00[EUR][1000 genomes]
rs1880270	1.00[EUR][1000 genomes]
rs1880271	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2328862	1.00[EUR][1000 genomes]
rs2690043	1.00[EUR][1000 genomes]
rs2690044	1.00[EUR][1000 genomes]
rs2690045	1.00[EUR][1000 genomes]
rs2690046	1.00[EUR][1000 genomes]
rs2690048	1.00[EUR][1000 genomes]
rs2690049	1.00[EUR][1000 genomes]
rs2690050	1.00[EUR][1000 genomes]
rs2690051	1.00[EUR][1000 genomes]
rs2690052	1.00[EUR][1000 genomes]
rs2690053	1.00[EUR][1000 genomes]
rs2690058	1.00[EUR][1000 genomes]
rs2690062	1.00[EUR][1000 genomes]
rs2690066	1.00[EUR][1000 genomes]
rs2690069	1.00[EUR][1000 genomes]
rs2690073	1.00[EUR][1000 genomes]
rs2690075	1.00[EUR][1000 genomes]
rs2690076	1.00[EUR][1000 genomes]
rs2690102	1.00[EUR][1000 genomes]
rs2690119	0.83[AFR][1000 genomes]
rs2690122	0.88[AFR][1000 genomes]
rs2690124	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs2744252	1.00[EUR][1000 genomes]
rs2744253	1.00[EUR][1000 genomes]
rs2744255	1.00[EUR][1000 genomes]
rs2744259	1.00[EUR][1000 genomes]
rs2744260	1.00[EUR][1000 genomes]
rs2744262	1.00[EUR][1000 genomes]
rs2744263	1.00[EUR][1000 genomes]
rs2744265	1.00[EUR][1000 genomes]
rs2744266	1.00[EUR][1000 genomes]
rs2744275	1.00[EUR][1000 genomes]
rs2744276	1.00[EUR][1000 genomes]
rs2744277	1.00[EUR][1000 genomes]
rs2744278	1.00[EUR][1000 genomes]
rs2744279	1.00[EUR][1000 genomes]
rs2744280	1.00[EUR][1000 genomes]
rs2744285	1.00[EUR][1000 genomes]
rs2744286	1.00[EUR][1000 genomes]
rs2744291	1.00[EUR][1000 genomes]
rs2744292	0.83[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2744295	0.83[AFR][1000 genomes]
rs34935689	1.00[EUR][1000 genomes]
rs940405	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	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25305000-25324400	Weak transcription	Left Ventricle	heart
2	chr6:25306600-25331400	Weak transcription	Spleen	Spleen
3	chr6:25310400-25319400	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr6:25312000-25324200	Weak transcription	Esophagus	oesophagus
5	chr6:25312000-25324200	Weak transcription	Pancreas	Pancrea
6	chr6:25313400-25329800	Weak transcription	Primary T cells from cord blood	blood
7	chr6:25313600-25320200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:25313800-25322800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr6:25313800-25325800	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr6:25313800-25326800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:25313800-25331400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr6:25314000-25318800	Weak transcription	Small Intestine	intestine
13	chr6:25314000-25325000	Weak transcription	Placenta	Placenta
14	chr6:25314200-25319200	Weak transcription	Thymus	Thymus
15	chr6:25314800-25319000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr6:25315400-25329600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:25315800-25324200	Weak transcription	Hela-S3	cervix
18	chr6:25316000-25320200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr6:25316000-25320400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr6:25316200-25319000	Weak transcription	Fetal Brain Female	brain
21	chr6:25316200-25319000	Weak transcription	Fetal Intestine Small	intestine
22	chr6:25316200-25320400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr6:25316200-25326800	Weak transcription	Gastric	stomach
24	chr6:25316400-25318800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr6:25316400-25326600	Weak transcription	Fetal Kidney	kidney
26	chr6:25316600-25319000	Weak transcription	Duodenum Mucosa	Duodenum
27	chr6:25316600-25319600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr6:25316600-25324200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:25317200-25319000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:25317200-25324200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr6:25317200-25324200	Weak transcription	Aorta	Aorta
32	chr6:25317400-25319000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr6:25317400-25320200	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr6:25317400-25320400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:25317400-25324000	Weak transcription	Fetal Intestine Large	intestine
36	chr6:25317800-25319000	Enhancers	Right Atrium	heart
37	chr6:25318000-25321600	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr6:25318200-25319000	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr6:25318400-25318600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr6:25318400-25318600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr6:25318400-25318600	Enhancers	Lung	lung
42	chr6:25318400-25319000	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr6:25318400-25319000	Enhancers	Ovary	ovary
44	chr6:25318400-25319000	Enhancers	HSMMtube	muscle
45	chr6:25318400-25319200	Enhancers	H1 Cell Line	embryonic stem cell
46	chr6:25318400-25319200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr6:25318400-25319600	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr6:25318400-25321200	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr6:25318400-25321200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr6:25318400-25321600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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