Variant report

Variant	rs2561427
Chromosome Location	chr6:39156460-39156461
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:39152659..39161573-chr6:39191951..39198831,12	K562	blood:
2	chr20:52577489..52580206-chr6:39156376..39158164,2	MCF-7	breast:
3	chr6:39155353..39158584-chr6:39158946..39166191,7	K562	blood:
4	chr6:39146393..39149644-chr6:39153708..39157375,4	K562	blood:
5	chr6:39155493..39158185-chr6:39159701..39165340,4	K562	blood:
6	chr6:39154121..39155675-chr6:39156063..39158781,2	K562	blood:
7	chr6:39136404..39138068-chr6:39155410..39157710,2	K562	blood:
8	chr6:39154908..39158754-chr6:39195824..39198738,4	K562	blood:
9	chr6:39150201..39152750-chr6:39156185..39158678,2	K562	blood:
10	chr6:39156141..39158653-chr6:39184593..39186726,2	MCF-7	breast:
11	chr6:39009574..39011759-chr6:39155267..39157602,2	K562	blood:
12	chr6:39138230..39140824-chr6:39155196..39157727,3	K562	blood:
13	chr6:39155283..39157120-chr6:39186284..39188129,2	K562	blood:
14	chr6:39156367..39160126-chr6:39192413..39195568,3	K562	blood:
15	chr6:39139089..39141843-chr6:39153750..39157319,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000164626	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1465569	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2561424	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2561426	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2815096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6458104	1.00[CEU][hapmap]
rs6902597	1.00[CEU][hapmap]
rs890923	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][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	nsv1028088	chr6:38821047-39163549	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv538205	chr6:38821047-39163549	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv830644	chr6:39116530-39325980	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1022974	chr6:39120271-39277553	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39139600-39157600	Weak transcription	Ovary	ovary
2	chr6:39146200-39160400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:39146600-39157400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr6:39148600-39157000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:39149000-39168000	Weak transcription	Fetal Kidney	kidney
6	chr6:39150000-39158800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:39150200-39157600	Weak transcription	Spleen	Spleen
8	chr6:39150600-39193800	Genic enhancers	Fetal Intestine Small	intestine
9	chr6:39150800-39158400	Enhancers	Stomach Mucosa	stomach
10	chr6:39151000-39156600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:39151000-39157200	Enhancers	Duodenum Mucosa	Duodenum
12	chr6:39151000-39165200	Strong transcription	H9 Cell Line	embryonic stem cell
13	chr6:39151200-39156800	Enhancers	Colonic Mucosa	Colon
14	chr6:39151400-39162200	Weak transcription	Thymus	Thymus
15	chr6:39151600-39161000	Strong transcription	Fetal Stomach	stomach
16	chr6:39153200-39162000	Genic enhancers	Placenta	Placenta
17	chr6:39153400-39157600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr6:39153400-39158000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:39154000-39157600	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr6:39154000-39157600	Strong transcription	Liver	Liver
21	chr6:39154200-39157200	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr6:39154200-39159800	Enhancers	Fetal Muscle Trunk	muscle
23	chr6:39154200-39164200	Genic enhancers	Fetal Intestine Large	intestine
24	chr6:39154400-39156800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr6:39154400-39162400	Weak transcription	Hela-S3	cervix
26	chr6:39154400-39164400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr6:39155000-39157000	Enhancers	Esophagus	oesophagus
28	chr6:39155200-39156600	Enhancers	HSMMtube	muscle
29	chr6:39155400-39156600	Enhancers	HSMM	muscle
30	chr6:39155400-39157000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr6:39155400-39158600	Enhancers	Fetal Muscle Leg	muscle
32	chr6:39155400-39172400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr6:39155600-39156600	Enhancers	A549	lung
34	chr6:39155600-39156800	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr6:39155600-39164000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr6:39155600-39166600	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr6:39155800-39157400	Weak transcription	Lung	lung
38	chr6:39155800-39157600	Weak transcription	Pancreas	Pancrea
39	chr6:39155800-39158400	Weak transcription	Colon Smooth Muscle	Colon
40	chr6:39155800-39160400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr6:39156000-39156800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr6:39156000-39157600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr6:39156000-39158000	Genic enhancers	Fetal Thymus	thymus
44	chr6:39156000-39160400	Weak transcription	Brain Substantia Nigra	brain
45	chr6:39156200-39156600	Genic enhancers	Gastric	stomach
46	chr6:39156200-39156600	Weak transcription	Small Intestine	intestine
47	chr6:39156200-39156800	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr6:39156200-39156800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr6:39156200-39157000	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr6:39156200-39158400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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