Variant report

Variant	rs6777535
Chromosome Location	chr3:119197016-119197017
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	chr3:119185648..119192167-chr3:119194088..119200916,11	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TIMMDC1-1	chr3:119196970-119197321	NONHSAT091388

Variant related genes	Relation type
ENSG00000176142	Chromatin interaction
ENSG00000163389	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1060569	0.94[ASN][1000 genomes]
rs13080905	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1797839	0.88[ASN][1000 genomes]
rs1900742	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1919586	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1919590	0.98[ASN][1000 genomes]
rs1967621	1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs1976919	0.94[ASN][1000 genomes]
rs2177812	0.94[ASN][1000 genomes]
rs3732413	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3732419	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs3814397	0.85[ASN][1000 genomes]
rs4687855	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4687860	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688005	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4688007	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4688008	0.94[ASN][1000 genomes]
rs4688012	1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs4688014	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6414282	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6414283	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6438528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6438529	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6438530	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6438531	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6438532	0.95[YRI][hapmap]
rs6438535	1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs6778945	0.87[ASN][1000 genomes]
rs6794822	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6794833	0.90[AFR][1000 genomes]
rs6796970	0.98[ASN][1000 genomes]
rs6799691	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs71618795	0.83[EUR][1000 genomes]
rs727905	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7430798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7621259	0.94[ASN][1000 genomes]
rs7628626	1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs7630587	0.98[ASN][1000 genomes]
rs7642502	1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs9289129	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9809155	0.98[ASN][1000 genomes]
rs9836627	1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs9850447	0.87[ASN][1000 genomes]
rs9867768	0.89[CHB][hapmap];0.87[ASN][1000 genomes]
rs9873196	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs9874480	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9877854	1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6777535	KTELC1	cis	multi-tissue	Pritchard
rs6777535	KTELC1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119188400-119216200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:119188400-119216800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:119188600-119198000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:119188600-119216200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:119188800-119216200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:119189000-119198000	Weak transcription	HSMM	muscle
7	chr3:119189000-119198200	Weak transcription	NH-A	brain
8	chr3:119189000-119199200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:119189000-119204400	Weak transcription	NHDF-Ad	bronchial
10	chr3:119189000-119216200	Weak transcription	Stomach Mucosa	stomach
11	chr3:119189000-119216200	Weak transcription	HUVEC	blood vessel
12	chr3:119189000-119216600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:119189200-119199000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:119189200-119199600	Weak transcription	HMEC	breast
15	chr3:119189200-119203000	Weak transcription	Fetal Kidney	kidney
16	chr3:119189400-119201800	Strong transcription	Fetal Stomach	stomach
17	chr3:119189600-119205400	Weak transcription	Hela-S3	cervix
18	chr3:119189600-119209200	Strong transcription	Primary B cells from cord blood	blood
19	chr3:119189600-119211800	Strong transcription	Primary B cells from peripheral blood	blood
20	chr3:119189600-119211800	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr3:119189800-119198800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:119189800-119199000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:119189800-119200800	Strong transcription	Fetal Thymus	thymus
24	chr3:119189800-119210000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:119189800-119211400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr3:119189800-119212200	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr3:119189800-119216000	Weak transcription	Fetal Heart	heart
28	chr3:119190000-119201200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr3:119190000-119201800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:119190000-119202000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:119190000-119211800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr3:119190000-119212200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:119190000-119212200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:119190200-119200200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
35	chr3:119190400-119199200	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr3:119190400-119212200	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr3:119190600-119199200	Strong transcription	Duodenum Mucosa	Duodenum
38	chr3:119190600-119204800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr3:119190600-119211800	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr3:119190600-119212000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr3:119190800-119199800	Weak transcription	Fetal Lung	lung
42	chr3:119190800-119204200	Weak transcription	A549	lung
43	chr3:119190800-119204200	Weak transcription	HSMMtube	muscle
44	chr3:119190800-119205000	Weak transcription	Psoas Muscle	Psoas
45	chr3:119190800-119216400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr3:119191000-119198000	Weak transcription	NHEK	skin
47	chr3:119191000-119203200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr3:119191000-119216400	Weak transcription	Fetal Brain Male	brain
49	chr3:119192000-119209800	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr3:119192400-119207200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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