Variant report

Variant	rs35003355
Chromosome Location	chr2:211344088-211344089
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:211340873..211343591-chr2:211343599..211345221,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115365	Chromatin interaction
ENSG00000021826	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10184506	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10195425	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12694198	0.95[ASN][1000 genomes]
rs12694200	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13005638	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1509816	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1858194	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1858195	0.83[EUR][1000 genomes]
rs2160851	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2287426	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2287427	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2370962	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2664239	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34374637	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3732058	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3755185	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3755186	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3755187	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3770686	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3770688	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3770693	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3770696	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3845634	0.81[AMR][1000 genomes]
rs4672580	0.82[EUR][1000 genomes]
rs4672581	0.82[EUR][1000 genomes]
rs4672582	0.82[EUR][1000 genomes]
rs57718949	0.84[AMR][1000 genomes]
rs6749711	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6752530	0.81[AMR][1000 genomes]
rs7590759	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs759688	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3398091	chr2:211315261-211634200	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35003355	LANCL1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:211341600-211344800	Weak transcription	Spleen	Spleen
2	chr2:211341600-211347800	Weak transcription	Gastric	stomach
3	chr2:211341600-211348800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:211341600-211348800	Weak transcription	Pancreas	Pancrea
5	chr2:211341800-211345000	Weak transcription	Fetal Muscle Leg	muscle
6	chr2:211342200-211344800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:211342400-211344800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr2:211342400-211346400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:211342600-211344800	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr2:211342600-211344800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr2:211342600-211346200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:211342600-211348000	Weak transcription	Fetal Intestine Small	intestine
13	chr2:211342800-211346200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr2:211342800-211346200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr2:211343000-211344800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr2:211343000-211344800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr2:211343000-211345800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr2:211343000-211346000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr2:211343000-211346200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr2:211343000-211355200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:211343200-211344800	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr2:211343200-211344800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr2:211343200-211344800	Weak transcription	HMEC	breast
24	chr2:211343200-211345800	Weak transcription	Hela-S3	cervix
25	chr2:211343200-211346200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr2:211343200-211348000	Weak transcription	Ovary	ovary
27	chr2:211343400-211344600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr2:211343400-211344800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr2:211343400-211344800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr2:211343400-211346600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr2:211343400-211347800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:211343400-211363600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:211343600-211344800	Weak transcription	NHEK	skin
34	chr2:211343600-211346200	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr2:211343800-211346400	Weak transcription	HSMM	muscle
36	chr2:211344000-211344800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr2:211344000-211344800	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr2:211344000-211344800	Weak transcription	K562	blood
39	chr2:211344000-211348800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr2:211344000-211350800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links