Variant report

Variant	rs11121521
Chromosome Location	chr1:10198217-10198218
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:10001858..10004296-chr1:10197406..10200222,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162441	Chromatin interaction
ENSG00000173614	Chromatin interaction
ENSG00000228150	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12070814	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12092513	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4415569	1.00[ASN][1000 genomes]
rs61782920	1.00[ASN][1000 genomes]
rs61782922	1.00[ASN][1000 genomes]
rs61782923	1.00[ASN][1000 genomes]
rs61782937	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6673887	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6685910	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687550	1.00[ASN][1000 genomes]
rs6688779	1.00[ASN][1000 genomes]
rs6691957	1.00[ASN][1000 genomes]
rs7538883	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541780	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[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	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv527217	chr1:10093457-10257167	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv522629	chr1:10125765-10239197	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	nsv525216	chr1:10195940-10200574	Strong transcription Weak transcription ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11121521	LZIC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10163400-10219000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:10164000-10227400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:10167600-10207400	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr1:10173000-10199400	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr1:10175000-10207200	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr1:10180000-10211200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr1:10181000-10199600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:10182200-10231200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:10182400-10229400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:10182800-10211400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:10182800-10221000	Weak transcription	Fetal Brain Male	brain
12	chr1:10182800-10231400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr1:10184000-10235000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:10185000-10201800	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:10185200-10199200	Strong transcription	Duodenum Mucosa	Duodenum
16	chr1:10185200-10201200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:10185400-10204400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr1:10185400-10207400	Strong transcription	Adipose Nuclei	Adipose
19	chr1:10185800-10211400	Weak transcription	A549	lung
20	chr1:10186000-10205800	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr1:10186200-10207800	Strong transcription	Fetal Intestine Large	intestine
22	chr1:10186400-10199400	Strong transcription	Fetal Muscle Leg	muscle
23	chr1:10186400-10207400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:10186600-10204200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:10186600-10207200	Strong transcription	Liver	Liver
26	chr1:10186600-10207800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:10186600-10207800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:10186800-10198800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:10186800-10201800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:10186800-10202000	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr1:10187000-10201600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:10187600-10202000	Strong transcription	Placenta	Placenta
33	chr1:10188000-10200000	Strong transcription	Fetal Brain Female	brain
34	chr1:10188200-10199600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:10188400-10200200	Strong transcription	Fetal Intestine Small	intestine
36	chr1:10188400-10208200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr1:10188400-10208600	Strong transcription	Fetal Stomach	stomach
38	chr1:10188600-10201600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:10188600-10204200	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:10188800-10199800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr1:10189400-10201200	Strong transcription	Fetal Lung	lung
42	chr1:10190200-10199400	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr1:10191200-10200400	Weak transcription	HepG2	liver
44	chr1:10191200-10225000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr1:10191200-10239600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr1:10191800-10203600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr1:10191800-10209200	Weak transcription	Fetal Heart	heart
48	chr1:10191800-10215600	Weak transcription	Psoas Muscle	Psoas
49	chr1:10193200-10200600	Weak transcription	HMEC	breast
50	chr1:10193200-10201600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

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