Variant report

Variant	rs4971002
Chromosome Location	chr1:151103790-151103791
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151102270..151104122-chr1:151117546..151119575,3	K562	blood:
2	chr1:151103786..151106331-chr1:151117499..151120768,3	MCF-7	breast:
3	chr1:151100859..151103920-chr1:151107452..151111935,4	MCF-7	breast:
4	chr1:151099788..151103928-chr1:151106315..151110197,5	K562	blood:
5	chr1:151101938..151104431-chr1:151107566..151109145,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SEMA6C-1	chr1:151102536-151104086	NONHSAT006361
2	lnc-SEMA6C-1	chr1:151102551-151104086	ENSG00000261168.1

No data

Variant related genes	Relation type
ENSG00000143434	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10788798	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10788799	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10788800	0.81[ASN][1000 genomes]
rs11204777	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11204778	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11204780	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12117163	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1524773	0.84[ASN][1000 genomes]
rs2140709	0.84[ASN][1000 genomes]
rs3738481	0.84[ASN][1000 genomes]
rs4357530	0.81[ASN][1000 genomes]
rs4970993	0.84[ASN][1000 genomes]
rs4970998	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4970999	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4971003	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4971005	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4971006	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4971007	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4971008	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5023311	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61819219	0.81[ASN][1000 genomes]
rs6656450	0.81[ASN][1000 genomes]
rs6668894	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6676190	0.81[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	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
5	nsv872422	chr1:151098077-151115186	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv872423	chr1:151100612-151115997	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4971002	BNIPL	cis	Thyroid	GTEx
rs4971002	LYSMD1	Cis_1M	lymphoblastoid	RTeQTL
rs4971002	BNIPL	cis	lung	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151061800-151105600	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr1:151079800-151106200	Weak transcription	HSMMtube	muscle
3	chr1:151079800-151114800	Weak transcription	HSMM	muscle
4	chr1:151090800-151105000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:151091200-151103800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr1:151097800-151105600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:151097800-151106000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:151103000-151104600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:151103200-151103800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
10	chr1:151103200-151104400	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr1:151103200-151104400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:151103200-151104400	Active TSS	Fetal Kidney	kidney
13	chr1:151103200-151104600	Active TSS	Brain Anterior Caudate	brain
14	chr1:151103200-151106000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
15	chr1:151103400-151103800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
16	chr1:151103400-151103800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr1:151103400-151103800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
18	chr1:151103400-151103800	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
19	chr1:151103400-151103800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:151103400-151103800	Flanking Active TSS	Fetal Intestine Large	intestine
21	chr1:151103400-151103800	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
22	chr1:151103400-151103800	Flanking Active TSS	Fetal Stomach	stomach
23	chr1:151103400-151103800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr1:151103400-151103800	Flanking Active TSS	Thymus	Thymus
25	chr1:151103400-151103800	Flanking Active TSS	NHEK	skin
26	chr1:151103400-151104000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:151103400-151104000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
28	chr1:151103400-151104000	Bivalent/Poised TSS	Colonic Mucosa	Colon
29	chr1:151103400-151104200	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
30	chr1:151103400-151104200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:151103400-151104200	Active TSS	Brain Angular Gyrus	brain
32	chr1:151103400-151104200	Active TSS	Fetal Heart	heart
33	chr1:151103400-151104200	Flanking Active TSS	Fetal Lung	lung
34	chr1:151103400-151104200	Flanking Active TSS	Fetal Thymus	thymus
35	chr1:151103400-151104400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr1:151103400-151104400	Flanking Active TSS	Primary B cells from peripheral blood	blood
37	chr1:151103400-151104400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
38	chr1:151103400-151104400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
39	chr1:151103400-151104400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
40	chr1:151103400-151104400	Active TSS	Aorta	Aorta
41	chr1:151103400-151104400	Active TSS	Brain Cingulate Gyrus	brain
42	chr1:151103400-151104400	Active TSS	Placenta Amnion	Placenta Amnion
43	chr1:151103400-151104400	Flanking Active TSS	NHDF-Ad	bronchial
44	chr1:151103400-151104400	Flanking Active TSS	NHLF	lung
45	chr1:151103400-151104600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:151103400-151104600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
47	chr1:151103400-151104600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:151103400-151104600	Flanking Active TSS	Duodenum Mucosa	Duodenum
49	chr1:151103400-151104600	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr1:151103400-151104600	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links