Variant report

Variant	rs6440998
Chromosome Location	chr3:155242117-155242118
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:155239458..155242156-chr3:155242242..155245000,2	MCF-7	breast:

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10936006	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10936014	0.81[JPT][hapmap]
rs12632699	0.86[JPT][hapmap]
rs1401695	0.85[JPT][hapmap]
rs1607590	0.85[JPT][hapmap]
rs1607591	0.86[JPT][hapmap]
rs173369	0.85[JPT][hapmap]
rs181696	0.95[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs183088	0.85[JPT][hapmap]
rs1878859	0.83[JPT][hapmap]
rs1879089	0.86[JPT][hapmap]
rs189639	0.86[JPT][hapmap]
rs1914799	0.86[JPT][hapmap]
rs2015945	0.85[JPT][hapmap]
rs2102897	0.80[JPT][hapmap]
rs2203885	0.81[JPT][hapmap]
rs2315589	0.81[JPT][hapmap]
rs28575712	0.88[AFR][1000 genomes]
rs359539	0.86[JPT][hapmap]
rs359540	0.86[JPT][hapmap]
rs359542	0.85[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs359549	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs359550	0.81[ASN][1000 genomes]
rs359551	0.86[JPT][hapmap]
rs359552	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs359553	0.86[JPT][hapmap]
rs359554	0.86[JPT][hapmap]
rs359556	0.86[JPT][hapmap]
rs359557	0.86[JPT][hapmap]
rs359561	0.85[JPT][hapmap]
rs359565	0.85[JPT][hapmap]
rs359566	0.86[JPT][hapmap]
rs359568	0.86[JPT][hapmap]
rs359569	0.86[JPT][hapmap]
rs359570	0.86[JPT][hapmap]
rs3908138	0.86[JPT][hapmap]
rs3908140	0.86[JPT][hapmap]
rs3908141	0.86[JPT][hapmap]
rs3908144	0.85[JPT][hapmap]
rs3914780	0.86[JPT][hapmap]
rs4125975	0.86[JPT][hapmap]
rs4401403	0.86[JPT][hapmap]
rs4680201	0.86[JPT][hapmap]
rs4680205	0.86[JPT][hapmap]
rs4680210	0.80[JPT][hapmap]
rs484663	0.86[JPT][hapmap]
rs500051	0.81[JPT][hapmap]
rs517971	0.86[JPT][hapmap]
rs521073	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs536008	0.86[JPT][hapmap]
rs569813	0.86[JPT][hapmap]
rs578492	0.86[JPT][hapmap]
rs628026	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6440994	0.97[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs6440995	0.97[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs6440996	0.92[ASN][1000 genomes]
rs6440997	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6441002	0.86[JPT][hapmap]
rs6441003	0.86[JPT][hapmap]
rs6441005	0.81[JPT][hapmap]
rs658283	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs673001	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6767886	0.86[JPT][hapmap]
rs6768777	0.85[JPT][hapmap]
rs6769807	0.80[JPT][hapmap]
rs6770715	0.87[TSI][hapmap]
rs6793225	0.86[JPT][hapmap]
rs7609669	0.86[JPT][hapmap]
rs7629025	0.86[JPT][hapmap]
rs7629557	0.85[JPT][hapmap]
rs7641141	0.86[JPT][hapmap]
rs783550	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9809924	0.84[JPT][hapmap]
rs9818926	0.95[JPT][hapmap]
rs9828161	0.86[JPT][hapmap]
rs9865998	0.86[JPT][hapmap]
rs9874559	0.86[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2763309	chr3:155193454-155256770	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6440998	PPM1L	cis	cerebellum	SCAN
rs6440998	PLCH1	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155200800-155251400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:155230600-155242800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:155230600-155243800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:155230600-155249000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:155230600-155271400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:155230800-155244400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:155230800-155248400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:155231200-155253000	Weak transcription	A549	lung
9	chr3:155232200-155253000	Weak transcription	Fetal Intestine Large	intestine
10	chr3:155232200-155258800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:155232200-155274000	Weak transcription	Pancreas	Pancrea
12	chr3:155232400-155244000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:155232400-155247000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr3:155232400-155250400	Weak transcription	Gastric	stomach
15	chr3:155235400-155249000	Weak transcription	Fetal Intestine Small	intestine
16	chr3:155236200-155249400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:155237000-155248800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:155238000-155249000	Strong transcription	Dnd41	blood
19	chr3:155239400-155244000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:155239800-155248200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:155241000-155245000	Strong transcription	Thymus	Thymus
22	chr3:155241200-155243800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:155241800-155243000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr3:155241800-155243000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:155241800-155248600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr3:155241800-155248800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr3:155241800-155248800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:155241800-155249000	Weak transcription	Fetal Thymus	thymus
29	chr3:155241800-155273000	Weak transcription	Duodenum Mucosa	Duodenum
30	chr3:155242000-155242400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr3:155242000-155248400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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