Variant report

Variant	rs6540767
Chromosome Location	chr1:212990108-212990109
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212987979..212990902-chr1:213030404..213032283,2	MCF-7	breast:
2	chr1:212965331..212966831-chr1:212989639..212991384,2	K562	blood:

Variant related genes	Relation type
ENSG00000203705	Chromatin interaction
ENSG00000162769	Chromatin interaction
ENSG00000198468	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10127613	0.87[EUR][1000 genomes]
rs1021994	0.80[ASN][1000 genomes]
rs1032962	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1032963	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1032964	0.91[EUR][1000 genomes]
rs1032965	0.84[ASN][1000 genomes]
rs10746436	0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs10779583	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10863992	0.84[EUR][1000 genomes]
rs10864002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10864003	0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs11120005	0.84[EUR][1000 genomes]
rs11120028	0.89[ASN][1000 genomes]
rs11120033	0.83[AFR][1000 genomes]
rs11120034	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11120038	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12038225	0.95[ASN][1000 genomes]
rs12124669	0.90[CHB][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12133194	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12239017	0.81[EUR][1000 genomes]
rs12568552	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12744555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12757944	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1507359	0.91[EUR][1000 genomes]
rs15702	1.00[CEU][hapmap];0.96[YRI][hapmap];0.91[EUR][1000 genomes]
rs1580991	0.83[EUR][1000 genomes]
rs1580992	0.83[EUR][1000 genomes]
rs1605420	0.80[EUR][1000 genomes]
rs1813705	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1848243	0.89[EUR][1000 genomes]
rs2292214	0.88[EUR][1000 genomes]
rs2456818	0.85[ASN][1000 genomes]
rs2456827	0.89[ASN][1000 genomes]
rs2456828	0.81[ASN][1000 genomes]
rs2884675	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3738800	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3738802	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3949369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4639827	0.91[EUR][1000 genomes]
rs4951464	0.87[ASN][1000 genomes]
rs4951639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6540766	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6665489	0.83[EUR][1000 genomes]
rs6670373	0.83[EUR][1000 genomes]
rs6670869	0.90[EUR][1000 genomes]
rs6678961	0.83[EUR][1000 genomes]
rs6681851	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6685864	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6686145	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6686164	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6689799	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6694887	0.91[EUR][1000 genomes]
rs6696870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6700465	0.91[EUR][1000 genomes]
rs6702544	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6703982	0.83[EUR][1000 genomes]
rs7513199	0.89[EUR][1000 genomes]
rs7513210	0.89[EUR][1000 genomes]
rs7513734	0.89[EUR][1000 genomes]
rs7513772	0.89[EUR][1000 genomes]
rs7514070	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7522100	0.91[EUR][1000 genomes]
rs7528303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535608	0.91[EUR][1000 genomes]
rs7538853	0.91[EUR][1000 genomes]
rs7543603	0.89[EUR][1000 genomes]
rs7547100	0.89[EUR][1000 genomes]
rs7555930	0.86[EUR][1000 genomes]

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	nsv1001637	chr1:212907611-213034606	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	esv2756884	chr1:212925429-213006397	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2758997	chr1:212925429-213006397	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6540767	TATDN3	cis	multi-tissue	Pritchard
rs6540767	FLVCR1-AS1	cis	Adipose Subcutaneous	GTEx
rs6540767	FLVCR1-AS1	cis	Whole Blood	GTEx
rs6540767	FLVCR1-AS1	cis	Esophagus Muscularis	GTEx
rs6540767	FLVCR1-AS1	cis	lung	GTEx
rs6540767	FLVCR1	Cis_1M	lymphoblastoid	RTeQTL
rs6540767	NSL1	Cis_1M	lymphoblastoid	RTeQTL
rs6540767	LQK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212965800-212992600	Weak transcription	Lung	lung
2	chr1:212966000-212997400	Weak transcription	Aorta	Aorta
3	chr1:212966400-212990200	Weak transcription	Right Ventricle	heart
4	chr1:212969600-212993000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:212971200-212990200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:212972400-212993600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:212972600-212990200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:212975800-212997800	Weak transcription	Brain Substantia Nigra	brain
9	chr1:212976000-212990200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr1:212976000-212990200	Weak transcription	Fetal Brain Female	brain
11	chr1:212976200-212998800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr1:212979200-212994200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:212979600-212992000	Weak transcription	Brain Anterior Caudate	brain
14	chr1:212979600-212993200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr1:212979600-213001000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:212980800-213001000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:212981000-212990400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr1:212981600-212990400	Weak transcription	Fetal Muscle Leg	muscle
19	chr1:212982400-212990400	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr1:212982600-212990400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:212982600-212992800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr1:212982800-212992200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:212982800-212992600	Weak transcription	Placenta	Placenta
24	chr1:212987000-212992200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:212987200-212993000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:212987400-212991200	Enhancers	Fetal Intestine Large	intestine
27	chr1:212988200-212990400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:212988200-212990600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr1:212988200-212992000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:212988200-212992600	Weak transcription	Primary B cells from cord blood	blood
31	chr1:212988400-212998800	Weak transcription	Adipose Nuclei	Adipose
32	chr1:212988600-212992400	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr1:212988600-212993000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr1:212988600-212993200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:212988600-212998400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:212988800-212990400	Weak transcription	Liver	Liver
37	chr1:212988800-212990400	Weak transcription	Left Ventricle	heart
38	chr1:212988800-212990600	Weak transcription	Primary T cells from cord blood	blood
39	chr1:212988800-212990600	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr1:212988800-212990600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr1:212988800-212990600	Enhancers	Pancreatic Islets	Pancreatic Islet
42	chr1:212988800-212991400	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr1:212988800-212992600	Weak transcription	GM12878-XiMat	blood
44	chr1:212988800-212993800	Weak transcription	Fetal Thymus	thymus
45	chr1:212989000-212990800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr1:212989000-212992000	Enhancers	HepG2	liver
47	chr1:212989000-212992200	Weak transcription	Dnd41	blood
48	chr1:212989000-212992400	Weak transcription	Primary hematopoietic stem cells	blood
49	chr1:212989000-212992400	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr1:212989200-212993400	Enhancers	Fetal Intestine Small	intestine

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