Variant report

Variant	rs6961429
Chromosome Location	chr7:27704400-27704401
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF1	chr7:27704383-27704540	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:27702844..27705316-chr7:27782990..27784557,2	K562	blood:
2	chr7:27702189..27703735-chr7:27703951..27706256,2	MCF-7	breast:
3	chr7:27699948..27706867-chr7:27775418..27784557,21	K562	blood:
4	chr7:27704178..27705871-chr7:27706001..27707559,2	MCF-7	breast:
5	chr7:27700432..27708426-chr7:27777901..27782637,20	K562	blood:
6	chr7:27702921..27706495-chr7:27708435..27711221,3	K562	blood:
7	chr7:27704274..27706195-chr7:27778944..27780462,2	MCF-7	breast:

No data

Variant related genes	Relation type
HIBADH	TF binding region
ENSG00000106052	Chromatin interaction
ENSG00000229893	Chromatin interaction
ENSG00000106049	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs1009252	1.00[JPT][hapmap]
rs1014373	1.00[JPT][hapmap]
rs1015750	1.00[JPT][hapmap]
rs1030003	1.00[JPT][hapmap]
rs10447552	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1052724	1.00[JPT][hapmap]
rs1052741	1.00[JPT][hapmap]
rs10951172	1.00[JPT][hapmap]
rs10951175	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10951176	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1115346	0.87[ASN][1000 genomes]
rs11526176	1.00[JPT][hapmap]
rs11762342	0.87[ASN][1000 genomes]
rs11763449	0.87[ASN][1000 genomes]
rs11766457	0.93[ASN][1000 genomes]
rs11973492	0.87[ASN][1000 genomes]
rs12155430	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12164139	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12530626	1.00[JPT][hapmap]
rs12531952	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535844	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12537499	1.00[JPT][hapmap]
rs12540276	1.00[JPT][hapmap]
rs12665991	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12667235	1.00[JPT][hapmap]
rs12667610	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12668430	1.00[JPT][hapmap]
rs12670771	0.80[ASN][1000 genomes]
rs12672811	0.87[ASN][1000 genomes]
rs12700813	1.00[JPT][hapmap]
rs12700815	1.00[JPT][hapmap]
rs12700817	1.00[JPT][hapmap]
rs12700826	1.00[JPT][hapmap]
rs12700832	0.93[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs13226102	0.80[ASN][1000 genomes]
rs13227873	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs13237776	1.00[JPT][hapmap]
rs13242248	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13244903	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13246464	1.00[JPT][hapmap]
rs13308974	0.80[ASN][1000 genomes]
rs1357760	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1404276	1.00[JPT][hapmap]
rs1404278	1.00[JPT][hapmap]
rs1524530	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1524531	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1524533	1.00[JPT][hapmap]
rs1608664	1.00[JPT][hapmap]
rs17155546	1.00[JPT][hapmap]
rs1851913	1.00[JPT][hapmap]
rs1880370	1.00[JPT][hapmap]
rs1980329	1.00[JPT][hapmap]
rs2041714	1.00[JPT][hapmap]
rs2080245	1.00[JPT][hapmap]
rs2098315	1.00[JPT][hapmap]
rs2110526	1.00[JPT][hapmap]
rs2110528	1.00[JPT][hapmap]
rs2391452	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2391453	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3823946	0.88[CEU][hapmap]
rs3925338	1.00[JPT][hapmap]
rs4140899	1.00[JPT][hapmap]
rs42085	1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs42099	1.00[JPT][hapmap]
rs4348389	1.00[JPT][hapmap]
rs4719902	1.00[JPT][hapmap]
rs4722719	1.00[JPT][hapmap]
rs4722724	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4722728	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs56123216	0.81[ASN][1000 genomes]
rs56139857	0.87[ASN][1000 genomes]
rs58747588	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6415251	1.00[JPT][hapmap]
rs6462029	1.00[JPT][hapmap]
rs6462031	1.00[JPT][hapmap]
rs6462034	1.00[JPT][hapmap]
rs6462037	1.00[JPT][hapmap]
rs6462038	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6945993	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6946075	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6947731	1.00[JPT][hapmap]
rs6948460	0.87[ASN][1000 genomes]
rs6948814	1.00[JPT][hapmap]
rs6955074	1.00[JPT][hapmap]
rs6958747	1.00[JPT][hapmap]
rs6959495	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6960834	1.00[JPT][hapmap]
rs6963421	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6964190	1.00[JPT][hapmap]
rs6966587	0.87[ASN][1000 genomes]
rs6970104	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6974387	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6974932	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6980382	1.00[JPT][hapmap]
rs723699	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs723700	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7455882	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7778320	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7783447	1.00[JPT][hapmap]
rs7789788	1.00[JPT][hapmap]
rs7790498	0.80[ASN][1000 genomes]
rs7794292	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap]
rs7805086	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7806812	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9639552	1.00[JPT][hapmap]
rs9639553	1.00[JPT][hapmap]
rs978447	1.00[JPT][hapmap]
rs986706	1.00[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	nsv949025	chr7:27578167-28075172	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6961429	SNX10	cis	cerebellum	SCAN
rs6961429	TAX1BP1	cis	cerebellum	SCAN
rs6961429	SCRN1	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27703200-27704800	Enhancers	Stomach Mucosa	stomach
2	chr7:27703200-27708200	Weak transcription	Colon Smooth Muscle	Colon
3	chr7:27703400-27705400	Enhancers	Placenta	Placenta
4	chr7:27703400-27706200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr7:27703600-27704800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr7:27703600-27708000	Weak transcription	Right Atrium	heart
7	chr7:27704000-27705000	Enhancers	HepG2	liver
8	chr7:27704200-27704800	Enhancers	HUVEC	blood vessel
9	chr7:27704200-27705200	Enhancers	K562	blood
10	chr7:27704200-27711000	Weak transcription	Duodenum Mucosa	Duodenum

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