Variant report

Variant	rs3912257
Chromosome Location	chr2:180855863-180855864
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:180855717..180856981-chr2:180941679..180942512,4	MCF-7	breast:
2	chr2:180854369..180856319-chr2:180869761..180872424,2	MCF-7	breast:
3	chr2:180854973..180857186-chr2:180866635..180869075,2	MCF-7	breast:
4	chr2:180828665..180830720-chr2:180855146..180856897,2	MCF-7	breast:
5	chr2:180846497..180849281-chr2:180854142..180856276,3	K562	blood:
6	chr2:180853987..180858139-chr2:180866524..180870001,3	MCF-7	breast:
7	chr2:180854938..180857526-chr2:180942782..180945485,2	MCF-7	breast:
8	chr2:180844029..180846342-chr2:180854790..180856297,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000163510	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1046356	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10497555	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.82[YRI][hapmap];0.98[ASN][1000 genomes]
rs12613483	0.85[ASN][1000 genomes]
rs12618422	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12621365	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12623020	0.85[ASN][1000 genomes]
rs12693216	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs16823586	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16867114	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16867119	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16867125	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs16867133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16867136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16867140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs259808	0.87[ASN][1000 genomes]
rs262279	0.96[ASN][1000 genomes]
rs3738943	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3768837	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3768839	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3845695	0.87[ASN][1000 genomes]
rs3845697	0.85[ASN][1000 genomes]
rs3845702	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3907347	0.85[ASN][1000 genomes]
rs3914458	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4893886	0.91[ASN][1000 genomes]
rs56213876	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6433822	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6726846	0.81[ASN][1000 genomes]
rs72958832	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72958838	0.84[ASN][1000 genomes]
rs72958887	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72960663	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72960669	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72960671	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72960679	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs818659	0.93[ASN][1000 genomes]
rs9989852	0.92[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	nsv875472	chr2:180696414-181024926	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	nsv875473	chr2:180696414-181055597	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1006598	chr2:180766983-180923051	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS 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	3 gene(s)	inside rSNPs	diseases
4	nsv531444	chr2:180796233-181434590	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180807000-180858400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr2:180808200-180860400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:180809000-180856000	Weak transcription	Fetal Stomach	stomach
4	chr2:180809400-180871000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:180811200-180856200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:180813400-180868200	Weak transcription	Stomach Mucosa	stomach
7	chr2:180816800-180860400	Weak transcription	Right Ventricle	heart
8	chr2:180816800-180868400	Weak transcription	Pancreas	Pancrea
9	chr2:180816800-180869000	Weak transcription	Spleen	Spleen
10	chr2:180816800-180870600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:180817200-180860400	Weak transcription	Aorta	Aorta
12	chr2:180817200-180860400	Weak transcription	Gastric	stomach
13	chr2:180819000-180871000	Weak transcription	Esophagus	oesophagus
14	chr2:180821600-180858800	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr2:180822200-180858200	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr2:180823400-180870600	Weak transcription	Fetal Intestine Small	intestine
17	chr2:180829400-180856000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr2:180829600-180871200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:180830200-180857600	Weak transcription	Fetal Heart	heart
20	chr2:180830800-180871000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr2:180831000-180856000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:180831000-180860400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr2:180832800-180860200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr2:180834200-180858200	Strong transcription	Primary B cells from cord blood	blood
25	chr2:180836800-180870400	Weak transcription	A549	lung
26	chr2:180839800-180870400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr2:180840600-180858200	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr2:180840600-180858200	Strong transcription	Dnd41	blood
29	chr2:180841000-180858200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:180843000-180870200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr2:180846800-180856400	Weak transcription	Osteobl	bone
32	chr2:180846800-180867000	Weak transcription	Colon Smooth Muscle	Colon
33	chr2:180846800-180869800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr2:180847000-180856400	Weak transcription	Brain Germinal Matrix	brain
35	chr2:180847600-180866200	Weak transcription	Psoas Muscle	Psoas
36	chr2:180848400-180858200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr2:180849000-180856600	Weak transcription	Fetal Brain Male	brain
38	chr2:180849000-180858200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:180849000-180869600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr2:180849400-180856400	Weak transcription	NHLF	lung
41	chr2:180850400-180862200	Weak transcription	Small Intestine	intestine
42	chr2:180850600-180870800	Weak transcription	HSMMtube	muscle
43	chr2:180851000-180870200	Weak transcription	Hela-S3	cervix
44	chr2:180851600-180856400	Weak transcription	Fetal Brain Female	brain
45	chr2:180851600-180870400	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr2:180851800-180857200	Weak transcription	Brain Substantia Nigra	brain
47	chr2:180851800-180870400	Weak transcription	HUVEC	blood vessel
48	chr2:180852000-180856000	Weak transcription	Stomach Smooth Muscle	stomach
49	chr2:180852000-180856200	Weak transcription	Brain Anterior Caudate	brain
50	chr2:180852000-180857400	Weak transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links