Variant report

Variant	rs6696019
Chromosome Location	chr1:155864977-155864978
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	chr1:155864077..155867922-chr1:155886880..155891317,4	MCF-7	breast:
2	chr1:155862181..155863978-chr1:155864920..155867045,2	K562	blood:

Variant related genes	Relation type
ENSG00000207475	Chromatin interaction
ENSG00000132680	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10796955	0.95[CEU][hapmap];0.80[AMR][1000 genomes]
rs10908483	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1111102	0.81[CEU][hapmap]
rs11264426	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs11585845	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs12026057	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12037177	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12080846	0.84[AFR][1000 genomes]
rs12091273	0.80[AFR][1000 genomes]
rs12091361	0.83[AFR][1000 genomes]
rs12118795	0.86[CEU][hapmap]
rs12144175	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12568523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs1889532	0.95[CEU][hapmap];0.80[AMR][1000 genomes]
rs1889533	0.80[AMR][1000 genomes]
rs2016251	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2282301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297649	1.00[CEU][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes]
rs2364403	0.85[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs4661218	0.95[CEU][hapmap]
rs66466805	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66669006	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6667652	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6670477	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6670493	0.95[CEU][hapmap]
rs72708205	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7528441	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7534858	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs7545308	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs867548	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs867549	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs867550	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs915178	0.81[CEU][hapmap]
rs915181	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs928596	0.95[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	esv3423892	chr1:155664084-155901487	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers 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	28 gene(s)	inside rSNPs	diseases
3	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6696019	RIT1	cis	Thyroid	GTEx
rs6696019	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs6696019	GON4L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155830000-155869000	Weak transcription	Gastric	stomach
2	chr1:155830400-155865800	Weak transcription	Esophagus	oesophagus
3	chr1:155830600-155866800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr1:155836400-155866400	Weak transcription	Primary B cells from cord blood	blood
5	chr1:155841800-155869200	Weak transcription	Right Ventricle	heart
6	chr1:155844400-155874000	Weak transcription	Fetal Brain Male	brain
7	chr1:155847600-155866400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr1:155850600-155873600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:155851400-155866000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:155851400-155866000	Weak transcription	Spleen	Spleen
11	chr1:155851400-155866400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr1:155851400-155867400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr1:155851600-155866800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr1:155851600-155870200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr1:155854200-155868600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:155854400-155866200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:155854400-155866400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:155854400-155873600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:155854800-155868800	Weak transcription	Ovary	ovary
20	chr1:155860200-155865000	Weak transcription	Fetal Brain Female	brain
21	chr1:155861400-155866000	Weak transcription	Pancreas	Pancrea
22	chr1:155861600-155866600	Weak transcription	GM12878-XiMat	blood
23	chr1:155861800-155866000	Weak transcription	Primary B cells from peripheral blood	blood
24	chr1:155862600-155866000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:155862600-155866000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr1:155862800-155873600	Weak transcription	Psoas Muscle	Psoas
27	chr1:155863000-155869600	Weak transcription	Fetal Heart	heart
28	chr1:155863200-155870000	Weak transcription	Colonic Mucosa	Colon
29	chr1:155863400-155865400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr1:155863400-155866200	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr1:155863400-155866400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:155863400-155867400	Weak transcription	Dnd41	blood
33	chr1:155863400-155868800	Weak transcription	Colon Smooth Muscle	Colon
34	chr1:155863400-155868800	Weak transcription	Left Ventricle	heart
35	chr1:155863400-155873600	Weak transcription	Stomach Mucosa	stomach
36	chr1:155863400-155880200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr1:155863600-155865800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:155863600-155865800	Weak transcription	Thymus	Thymus
39	chr1:155863600-155866000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr1:155863600-155866000	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr1:155863600-155866600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr1:155863600-155866600	Weak transcription	Brain Angular Gyrus	brain
43	chr1:155863600-155868400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:155863800-155865600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:155863800-155866000	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr1:155863800-155866000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr1:155863800-155868800	Weak transcription	Brain Substantia Nigra	brain
48	chr1:155863800-155874000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr1:155864000-155865200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:155864000-155865200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links