Variant report

Variant	rs61616404
Chromosome Location	chr2:47172426-47172427
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:47170300..47176373-chr2:47180929..47185322,6	MCF-7	breast:
2	chr2:47168340..47172583-chr2:47183123..47189203,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272814	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10495940	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55654964	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60630351	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60652723	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6717185	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6741399	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6759170	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72886646	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72886669	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72886689	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7556761	0.86[AFR][1000 genomes]
rs7570279	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47169400-47178800	Weak transcription	Ovary	ovary
2	chr2:47169400-47179000	Weak transcription	Gastric	stomach
3	chr2:47169600-47172800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr2:47169600-47175000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:47169600-47177600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:47169600-47177600	Weak transcription	Left Ventricle	heart
7	chr2:47169600-47178800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:47169600-47183600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:47169800-47172800	Weak transcription	Fetal Heart	heart
10	chr2:47169800-47177600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr2:47169800-47177600	Weak transcription	Fetal Lung	lung
12	chr2:47169800-47178200	Weak transcription	Fetal Brain Female	brain
13	chr2:47169800-47182000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:47169800-47182200	Weak transcription	Right Ventricle	heart
15	chr2:47169800-47214600	Weak transcription	Fetal Kidney	kidney
16	chr2:47170000-47177000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr2:47170000-47177400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr2:47170000-47177600	Weak transcription	Esophagus	oesophagus
19	chr2:47170000-47177800	Weak transcription	Liver	Liver
20	chr2:47170000-47177800	Weak transcription	NH-A	brain
21	chr2:47170000-47178800	Weak transcription	HSMMtube	muscle
22	chr2:47170000-47181600	Weak transcription	HUVEC	blood vessel
23	chr2:47170000-47182200	Weak transcription	Psoas Muscle	Psoas
24	chr2:47170200-47177600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:47170200-47181400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr2:47170400-47177400	Weak transcription	Fetal Intestine Large	intestine
27	chr2:47170600-47173400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr2:47170600-47173400	Weak transcription	HMEC	breast
29	chr2:47170600-47178800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr2:47170800-47173000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr2:47170800-47173400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:47170800-47173600	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr2:47170800-47176000	Strong transcription	Fetal Stomach	stomach
34	chr2:47170800-47177600	Weak transcription	K562	blood
35	chr2:47170800-47178200	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr2:47170800-47184000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr2:47171000-47172600	Weak transcription	Fetal Muscle Leg	muscle
38	chr2:47171000-47173200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr2:47171000-47173600	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr2:47171000-47174000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr2:47171000-47174400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr2:47171000-47176200	Enhancers	Primary hematopoietic stem cells	blood
43	chr2:47171000-47177600	Weak transcription	Aorta	Aorta
44	chr2:47171000-47177600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr2:47171000-47178200	Weak transcription	Colonic Mucosa	Colon
46	chr2:47171000-47178200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr2:47171000-47178400	Weak transcription	Stomach Mucosa	stomach
48	chr2:47171000-47182600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr2:47171200-47172800	Weak transcription	Duodenum Mucosa	Duodenum
50	chr2:47171200-47173200	Weak transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links