Variant report

Variant	rs6955064
Chromosome Location	chr7:102579571-102579572
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	chr7:102574165..102576596-chr7:102576864..102579639,2	K562	blood:

Variant related genes	Relation type
ENSG00000161040	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10487281	1.00[ASN][1000 genomes]
rs10487284	1.00[ASN][1000 genomes]
rs11496066	1.00[ASN][1000 genomes]
rs12113073	1.00[ASN][1000 genomes]
rs17135875	1.00[ASN][1000 genomes]
rs17135913	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17135916	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17474893	1.00[ASN][1000 genomes]
rs2041094	1.00[ASN][1000 genomes]
rs2228687	0.89[EUR][1000 genomes]
rs2411061	0.90[EUR][1000 genomes]
rs3893651	1.00[ASN][1000 genomes]
rs4377880	1.00[ASN][1000 genomes]
rs4398822	1.00[ASN][1000 genomes]
rs55681588	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55781834	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55849741	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55851590	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56314487	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56336567	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56692051	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6465886	0.86[EUR][1000 genomes]
rs66712128	0.89[EUR][1000 genomes]
rs6964296	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6968036	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs727175	1.00[ASN][1000 genomes]
rs73192015	1.00[ASN][1000 genomes]
rs73192019	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73192025	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73192026	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73714541	0.89[EUR][1000 genomes]
rs7779854	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7781557	1.00[ASN][1000 genomes]
rs7798582	0.89[EUR][1000 genomes]
rs7809047	1.00[ASN][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	nsv1016563	chr7:101912320-102695860	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1028438	chr7:101912320-102704135	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	esv2752138	chr7:102358320-102787135	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv464667	chr7:102486254-102624192	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv608060	chr7:102486254-102624192	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6955064	LRRC17	cis	Stomach	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102571400-102579600	Genic enhancers	HSMM	muscle
2	chr7:102571600-102581800	Weak transcription	Fetal Intestine Small	intestine
3	chr7:102573400-102579800	Genic enhancers	Fetal Lung	lung
4	chr7:102573800-102591400	Weak transcription	Pancreas	Pancrea
5	chr7:102574000-102592200	Weak transcription	Fetal Intestine Large	intestine
6	chr7:102574200-102579600	Weak transcription	Colon Smooth Muscle	Colon
7	chr7:102574600-102594400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr7:102574800-102579800	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr7:102575000-102584400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr7:102575000-102586000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr7:102575000-102586800	Weak transcription	NHLF	lung
12	chr7:102575400-102587000	Strong transcription	NH-A	brain
13	chr7:102575600-102581600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr7:102575600-102583000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:102575600-102585200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:102575600-102586800	Weak transcription	Osteobl	bone
17	chr7:102576000-102579800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr7:102576800-102582000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr7:102576800-102582400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr7:102576800-102582400	Weak transcription	NHDF-Ad	bronchial
21	chr7:102576800-102584000	Weak transcription	Fetal Muscle Leg	muscle
22	chr7:102576800-102584200	Weak transcription	Aorta	Aorta
23	chr7:102577000-102582400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr7:102577000-102582800	Weak transcription	Right Atrium	heart
25	chr7:102577200-102582400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr7:102577400-102582400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr7:102577600-102587400	Weak transcription	Fetal Kidney	kidney
28	chr7:102577800-102586400	Weak transcription	Fetal Brain Male	brain
29	chr7:102578200-102579800	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr7:102578200-102579800	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr7:102578400-102579800	Enhancers	Adipose Nuclei	Adipose
32	chr7:102578400-102584000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr7:102578600-102579600	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr7:102578600-102579800	Enhancers	HSMMtube	muscle
35	chr7:102578600-102581000	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr7:102578800-102579600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr7:102578800-102579800	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr7:102578800-102580200	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr7:102579000-102579600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr7:102579000-102579600	Enhancers	Stomach Mucosa	stomach
41	chr7:102579000-102579800	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr7:102579000-102579800	Enhancers	Fetal Heart	heart
43	chr7:102579000-102579800	Enhancers	Fetal Stomach	stomach
44	chr7:102579000-102580200	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr7:102579000-102585800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr7:102579200-102579800	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr7:102579400-102579600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr7:102579400-102579600	Enhancers	Stomach Smooth Muscle	stomach
49	chr7:102579400-102579600	Enhancers	K562	blood
50	chr7:102579400-102579800	Enhancers	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links