Variant report

Variant	rs906597
Chromosome Location	chr1:154822517-154822518
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:154803405..154804925-chr1:154821285..154823065,2	K562	blood:
2	chr1:154814172..154816492-chr1:154821493..154823120,2	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1061122	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.87[EUR][1000 genomes]
rs10908443	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1218554	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1218584	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1218585	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs1218587	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1218588	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1218589	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12760148	1.00[CHB][hapmap]
rs16836525	1.00[CHB][hapmap]
rs2878412	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes]
rs4845396	1.00[CHB][hapmap]
rs4845397	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4845402	1.00[CHB][hapmap]
rs4845675	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6682335	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs906596	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	nsv427797	chr1:154559115-154933717	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv432931	chr1:154794318-154855055	Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	esv29982	chr1:154818353-154882544	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv432942	chr1:154818353-154903047	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv432964	chr1:154820067-154849590	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv432953	chr1:154820067-154855055	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs906597	LENEP	cis	cerebellum	SCAN
rs906597	FLG2	cis	parietal	SCAN
rs906597	S100A7L2	cis	parietal	SCAN
rs906597	C1orf85	cis	parietal	SCAN
rs906597	BCAN	cis	parietal	SCAN
rs906597	PSMD4	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154803200-154824600	Enhancers	Fetal Brain Male	brain
2	chr1:154808400-154823600	Enhancers	Fetal Muscle Leg	muscle
3	chr1:154812400-154824400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:154813800-154822600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr1:154815800-154823200	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr1:154817800-154823200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
7	chr1:154819200-154828400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:154819400-154822600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:154819400-154824200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:154820000-154824000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:154820000-154826000	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr1:154820200-154822800	Enhancers	HSMMtube	muscle
13	chr1:154820600-154822600	Enhancers	Brain Angular Gyrus	brain
14	chr1:154820800-154822600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:154820800-154832600	Weak transcription	Right Atrium	heart
16	chr1:154821000-154822800	Enhancers	Brain Cingulate Gyrus	brain
17	chr1:154821000-154822800	Enhancers	Fetal Brain Female	brain
18	chr1:154821000-154823000	Enhancers	Brain Hippocampus Middle	brain
19	chr1:154821000-154823200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:154821000-154832000	Weak transcription	HSMM	muscle
21	chr1:154821000-154837200	Weak transcription	Colon Smooth Muscle	Colon
22	chr1:154821200-154822800	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr1:154821200-154828400	Weak transcription	Psoas Muscle	Psoas
24	chr1:154821200-154828400	Weak transcription	Spleen	Spleen
25	chr1:154821200-154828800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:154821400-154825200	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr1:154821600-154822800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:154821800-154823000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr1:154821800-154823200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr1:154821800-154823200	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr1:154821800-154823400	Enhancers	H1 Cell Line	embryonic stem cell
32	chr1:154821800-154823400	Enhancers	Brain Germinal Matrix	brain
33	chr1:154822000-154822600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr1:154822000-154822600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:154822000-154822800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
36	chr1:154822000-154823200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:154822000-154823400	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr1:154822000-154824200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr1:154822000-154828000	Weak transcription	Brain Substantia Nigra	brain
40	chr1:154822200-154822600	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr1:154822200-154823000	Enhancers	Brain Anterior Caudate	brain
42	chr1:154822200-154828000	Weak transcription	Fetal Stomach	stomach
43	chr1:154822400-154822800	Flanking Active TSS	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links