Variant report

Variant	rs3856378
Chromosome Location	chr2:127872347-127872348
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:127868348..127869960-chr2:127871605..127873219,2	MCF-7	breast:
2	chr2:127865657..127869658-chr2:127871080..127873352,3	K562	blood:
3	chr2:127853337..127855770-chr2:127871735..127873345,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC114783.1.1-4	chr2:127871993-127874626	NONHSAT074143

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10167189	0.97[ASN][1000 genomes]
rs11675682	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11679418	0.89[EUR][1000 genomes]
rs11693218	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12617750	0.86[EUR][1000 genomes]
rs13019394	0.87[EUR][1000 genomes]
rs2164871	0.84[EUR][1000 genomes]
rs4662705	0.85[EUR][1000 genomes]
rs4663094	0.85[EUR][1000 genomes]
rs4663101	0.90[ASN][1000 genomes]
rs4663102	0.90[ASN][1000 genomes]
rs4663103	0.90[ASN][1000 genomes]
rs6706041	0.85[EUR][1000 genomes]
rs6708935	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs6709337	0.84[EUR][1000 genomes]
rs6709706	0.85[EUR][1000 genomes]
rs6718147	0.85[EUR][1000 genomes]
rs6740232	0.90[ASN][1000 genomes]
rs6759813	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs730471	0.91[EUR][1000 genomes]
rs734115	0.87[EUR][1000 genomes]
rs754107	0.88[EUR][1000 genomes]
rs755639	0.88[EUR][1000 genomes]
rs7560621	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7601252	0.97[ASN][1000 genomes]
rs7602810	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999422	chr2:127464647-127956543	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1004930	chr2:127477369-127938234	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv875012	chr2:127800981-127895573	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1006112	chr2:127830117-128032546	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	esv2757832	chr2:127830943-128006514	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	esv2759090	chr2:127830943-128006514	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv1005149	chr2:127841930-127880106	Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1011378	chr2:127841930-128020546	Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
9	nsv999809	chr2:127841930-128032546	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
10	nsv1010669	chr2:127848860-128032546	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
11	nsv1003599	chr2:127871183-128059407	Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
12	nsv535920	chr2:127871183-128059407	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3856378	BIN1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:127865800-127873000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr2:127866200-127872400	Weak transcription	Fetal Intestine Large	intestine
3	chr2:127866200-127873200	Weak transcription	Gastric	stomach
4	chr2:127866800-127872600	Weak transcription	Fetal Muscle Trunk	muscle
5	chr2:127867200-127873000	Weak transcription	A549	lung
6	chr2:127867400-127874800	Weak transcription	Brain Anterior Caudate	brain
7	chr2:127869600-127872400	Weak transcription	Liver	Liver
8	chr2:127870000-127873000	Weak transcription	Brain Angular Gyrus	brain
9	chr2:127870000-127873000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr2:127870200-127873000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr2:127870600-127898400	Weak transcription	Right Atrium	heart
12	chr2:127871800-127873200	Weak transcription	Brain Substantia Nigra	brain
13	chr2:127872200-127872800	Enhancers	Spleen	Spleen
14	chr2:127872200-127876200	Enhancers	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links