Variant report

Variant	rs4845396
Chromosome Location	chr1:154828409-154828410
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	chr1:154827805..154830333-chr1:154834809..154836322,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1061122	1.00[CHB][hapmap]
rs10908443	1.00[CHB][hapmap]
rs11264275	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12044470	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12045303	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1218554	1.00[CHB][hapmap]
rs1218584	1.00[CHB][hapmap]
rs1218585	1.00[CHB][hapmap]
rs1218587	1.00[CHB][hapmap]
rs1218589	1.00[CHB][hapmap]
rs12760148	1.00[CHB][hapmap]
rs16836525	1.00[CHB][hapmap]
rs2878411	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2878412	1.00[CHB][hapmap]
rs4845397	1.00[CHB][hapmap]
rs4845402	1.00[CHB][hapmap]
rs4845676	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6426998	0.82[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6682335	1.00[CHB][hapmap]
rs906595	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs906596	1.00[CHB][hapmap]
rs906597	1.00[CHB][hapmap]

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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4845396	KCNN3	cis	parietal	SCAN
rs4845396	KCNN3	cis	cerebellum	SCAN
rs4845396	RIT1	cis	cerebellum	SCAN
rs4845396	PBXIP1	Cis_1M	lymphoblastoid	RTeQTL
rs4845396	C1orf230	cis	cerebellum	SCAN
rs4845396	BCAN	cis	parietal	SCAN
rs4845396	OTUD7B	cis	cerebellum	SCAN
rs4845396	ENSA	cis	parietal	SCAN
rs4845396	INTS3	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154820800-154832600	Weak transcription	Right Atrium	heart
2	chr1:154821000-154832000	Weak transcription	HSMM	muscle
3	chr1:154821000-154837200	Weak transcription	Colon Smooth Muscle	Colon
4	chr1:154821200-154828800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr1:154822600-154838000	Weak transcription	Brain Angular Gyrus	brain
6	chr1:154822800-154832200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:154823000-154828600	Weak transcription	Brain Hippocampus Middle	brain
8	chr1:154823000-154830600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:154823400-154832400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:154824400-154834200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:154827600-154839400	Enhancers	Fetal Brain Male	brain
12	chr1:154827800-154829400	Enhancers	Brain Germinal Matrix	brain
13	chr1:154827800-154831000	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr1:154827800-154833600	Enhancers	Fetal Muscle Leg	muscle
15	chr1:154828000-154828800	Enhancers	Fetal Lung	lung
16	chr1:154828000-154829000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:154828000-154829200	Enhancers	Brain Substantia Nigra	brain
18	chr1:154828000-154830400	Enhancers	Fetal Stomach	stomach
19	chr1:154828000-154833400	Enhancers	Brain Anterior Caudate	brain
20	chr1:154828200-154828600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr1:154828200-154829200	Enhancers	HSMMtube	muscle
22	chr1:154828200-154829600	Enhancers	Fetal Thymus	thymus
23	chr1:154828400-154828600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
24	chr1:154828400-154828800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:154828400-154828800	Enhancers	Brain Cingulate Gyrus	brain
26	chr1:154828400-154828800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr1:154828400-154829000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:154828400-154829200	Flanking Active TSS	Fetal Brain Female	brain
29	chr1:154828400-154829400	Enhancers	Psoas Muscle	Psoas
30	chr1:154828400-154829400	Enhancers	Spleen	Spleen
31	chr1:154828400-154829600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr1:154828400-154833400	Flanking Active TSS	GM12878-XiMat	blood

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