Variant report

Variant	rs6995598
Chromosome Location	chr8:129866274-129866275
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:129860905..129863737-chr8:129866151..129867802,2	MCF-7	breast:
2	chr8:129865860..129869579-chr8:129877876..129880689,4	K562	blood:
3	chr8:129861118..129862963-chr8:129865839..129868302,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10092273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10094688	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10103995	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10447999	0.90[EUR][1000 genomes]
rs10956447	0.96[EUR][1000 genomes]
rs10956448	0.96[EUR][1000 genomes]
rs10956449	0.95[EUR][1000 genomes]
rs10956450	0.93[EUR][1000 genomes]
rs11782234	0.89[EUR][1000 genomes]
rs11785020	0.87[EUR][1000 genomes]
rs12547429	0.95[EUR][1000 genomes]
rs12550594	0.95[EUR][1000 genomes]
rs12675522	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12676288	0.96[EUR][1000 genomes]
rs12677710	0.89[EUR][1000 genomes]
rs12677712	0.89[EUR][1000 genomes]
rs12678715	0.90[EUR][1000 genomes]
rs12679405	0.98[EUR][1000 genomes]
rs12680246	0.95[EUR][1000 genomes]
rs13276570	0.95[EUR][1000 genomes]
rs13277797	0.95[EUR][1000 genomes]
rs13281755	0.95[EUR][1000 genomes]
rs1356763	0.89[EUR][1000 genomes]
rs1441992	0.94[EUR][1000 genomes]
rs1519839	0.87[EUR][1000 genomes]
rs1519853	0.83[EUR][1000 genomes]
rs1519854	0.83[EUR][1000 genomes]
rs1519855	0.83[EUR][1000 genomes]
rs17239733	0.88[EUR][1000 genomes]
rs17240568	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17240784	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17241323	1.00[CEU][hapmap];0.81[JPT][hapmap];0.95[EUR][1000 genomes]
rs17819852	0.92[EUR][1000 genomes]
rs1879165	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2056313	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2894458	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35526947	0.81[EUR][1000 genomes]
rs35902990	0.85[EUR][1000 genomes]
rs4593504	1.00[CEU][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs4733652	0.89[EUR][1000 genomes]
rs4733656	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4733657	0.93[EUR][1000 genomes]
rs6996154	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6999288	0.89[EUR][1000 genomes]
rs7831440	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7842437	0.89[EUR][1000 genomes]
rs871502	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9656973	0.84[EUR][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	nsv612220	chr8:129859924-129866274	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv517445	chr8:129859924-129881299	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6995598	KCNQ3	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:129858600-129868800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr8:129860000-129867000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr8:129861200-129867200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr8:129862800-129866600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr8:129863000-129866600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr8:129863200-129866400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr8:129863200-129866800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr8:129863200-129866800	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr8:129864000-129866800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr8:129864200-129866400	Weak transcription	Dnd41	blood
11	chr8:129864200-129866600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr8:129864200-129866800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr8:129864200-129873200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr8:129864200-129873200	Weak transcription	NH-A	brain
15	chr8:129864400-129866600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr8:129864400-129866600	Weak transcription	Osteobl	bone
17	chr8:129864400-129873400	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr8:129864600-129866400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr8:129865600-129869000	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr8:129866200-129866600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr8:129866200-129868200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr8:129866200-129868400	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr8:129866200-129869200	Enhancers	NHDF-Ad	bronchial

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