Variant report

Variant	rs6953698
Chromosome Location	chr7:127739666-127739667
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	chr7:127737543..127740197-chr7:127740336..127742903,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12706825	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35045093	0.88[EUR][1000 genomes]
rs35361134	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4731395	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62484016	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6467159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6467160	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6467161	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6467162	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6467163	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6954161	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6954389	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs759710	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7780024	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7792971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7793071	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7803045	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7803473	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7811971	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022385	chr7:127246656-127971194	Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv539120	chr7:127246656-127971194	Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6953698	LRRC4	cis	parietal	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127707800-127742200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr7:127724000-127739800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr7:127724600-127743600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr7:127726000-127743600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr7:127727200-127740000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr7:127730000-127742800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr7:127730400-127740600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr7:127730400-127743800	Weak transcription	HSMM	muscle
9	chr7:127731400-127743600	Weak transcription	Brain Substantia Nigra	brain
10	chr7:127731800-127743600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr7:127732200-127743600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr7:127732800-127743600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr7:127733000-127740600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr7:127733200-127743600	Weak transcription	Primary B cells from cord blood	blood
15	chr7:127733200-127743800	Weak transcription	Small Intestine	intestine
16	chr7:127733400-127740400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr7:127733600-127743400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr7:127733600-127743600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr7:127733800-127740400	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr7:127733800-127743400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr7:127734000-127740400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr7:127734000-127741200	Weak transcription	Fetal Lung	lung
23	chr7:127734200-127743600	Weak transcription	NHDF-Ad	bronchial
24	chr7:127734400-127744000	Weak transcription	A549	lung
25	chr7:127734400-127748200	Weak transcription	Dnd41	blood
26	chr7:127734600-127740000	Weak transcription	HSMMtube	muscle
27	chr7:127734600-127743600	Weak transcription	Brain Hippocampus Middle	brain
28	chr7:127734600-127743600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr7:127734800-127740000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr7:127734800-127740400	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr7:127734800-127743600	Weak transcription	Brain Anterior Caudate	brain
32	chr7:127734800-127743600	Weak transcription	HUVEC	blood vessel
33	chr7:127735000-127739800	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr7:127735000-127740000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr7:127735000-127740600	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr7:127735000-127741200	Weak transcription	Aorta	Aorta
37	chr7:127735000-127743600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr7:127735000-127743600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr7:127735200-127740600	Weak transcription	Spleen	Spleen
40	chr7:127735200-127742400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr7:127735200-127743000	Weak transcription	Right Atrium	heart
42	chr7:127735600-127741800	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr7:127735800-127740400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr7:127735800-127740400	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr7:127735800-127740600	Weak transcription	Primary T cells from cord blood	blood
46	chr7:127735800-127743600	Weak transcription	Ovary	ovary
47	chr7:127736200-127743600	Weak transcription	HMEC	breast
48	chr7:127736400-127741600	Weak transcription	Fetal Thymus	thymus
49	chr7:127736400-127742400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr7:127736400-127743600	Weak transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links