Variant report

Variant	rs61826778
Chromosome Location	chr1:173963249-173963250
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	chr1:173961254..173963664-chr1:173990369..173993312,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224977	Chromatin interaction
ENSG00000135870	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs61827866	0.90[EUR][1000 genomes]
rs61827871	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs61828581	1.00[AFR][1000 genomes]
rs72711407	0.90[EUR][1000 genomes]
rs72711439	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv916960	chr1:173907804-174080248	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv872550	chr1:173913804-173964206	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv872551	chr1:173913804-174025660	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv831937	chr1:173949373-174131463	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
6	esv3692957	chr1:173960747-173967521	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61826778	MGC20647	trans	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173900000-173966600	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr1:173900000-173968200	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr1:173900200-173966400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:173900400-173964600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:173900800-173963800	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr1:173901600-173966400	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr1:173901600-173966400	Strong transcription	Dnd41	blood
8	chr1:173904000-173966400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:173909800-173974200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:173915600-173977800	Weak transcription	Stomach Mucosa	stomach
11	chr1:173931200-173965600	Weak transcription	Small Intestine	intestine
12	chr1:173931200-173969800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr1:173941000-173965000	Strong transcription	Fetal Thymus	thymus
14	chr1:173942200-173967400	Weak transcription	Fetal Heart	heart
15	chr1:173942200-173986200	Weak transcription	Fetal Brain Male	brain
16	chr1:173947000-173966000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:173949200-173970600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:173949600-173965600	Weak transcription	Esophagus	oesophagus
19	chr1:173949600-173970600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:173950600-173973400	Weak transcription	Psoas Muscle	Psoas
21	chr1:173952200-173967200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr1:173952800-173967600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:173953200-173974200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr1:173954600-173963600	Strong transcription	Fetal Intestine Large	intestine
25	chr1:173955600-173966200	Strong transcription	Primary B cells from peripheral blood	blood
26	chr1:173956200-173963800	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr1:173956200-173966400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:173957200-173963600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:173957800-173964200	Weak transcription	Fetal Brain Female	brain
30	chr1:173958000-173963600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr1:173958200-173963600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:173958200-173963800	Strong transcription	Fetal Muscle Trunk	muscle
33	chr1:173958200-173966400	Strong transcription	Fetal Intestine Small	intestine
34	chr1:173958200-173966400	Strong transcription	Fetal Stomach	stomach
35	chr1:173958400-173964200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr1:173958400-173967200	Weak transcription	NHLF	lung
37	chr1:173958600-173987200	Weak transcription	Gastric	stomach
38	chr1:173959800-173963400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr1:173959800-173963400	Strong transcription	Liver	Liver
40	chr1:173960000-173966000	Strong transcription	Adipose Nuclei	Adipose
41	chr1:173960400-173966400	Strong transcription	K562	blood
42	chr1:173960800-173970400	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr1:173962000-173964600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:173962000-173964800	Weak transcription	HUVEC	blood vessel
45	chr1:173962000-173965600	Weak transcription	Brain Hippocampus Middle	brain
46	chr1:173962000-173967400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr1:173962000-173967600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr1:173962000-173975000	Weak transcription	Right Ventricle	heart
49	chr1:173962000-173988400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr1:173962200-173964000	Weak transcription	GM12878-XiMat	blood

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