Variant report

Variant	rs9608936
Chromosome Location	chr22:30881245-30881246
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr22:30881175-30882004	HCT-116	colon:	n/a	chr22:30881538-30881559 chr22:30881546-30881556 chr22:30881545-30881558 chr22:30881544-30881560 chr22:30881512-30881521 chr22:30881543-30881561 chr22:30881549-30881558
2	RAD21	chr22:30881190-30881835	HCT-116	colon:	n/a	chr22:30881541-30881560 chr22:30881543-30881555 chr22:30881545-30881555 chr22:30881544-30881557
3	CTCF	chr22:30881211-30881300	Lung_OC	lung:	n/a	n/a
4	CTCF	chr22:30881210-30881285	GM19238	blood:	n/a	n/a
5	CTCF	chr22:30881203-30881256	GM19240	blood:	n/a	n/a
6	CTCF	chr22:30881228-30881274	GM12892	blood:	n/a	n/a
7	CTCF	chr22:30880760-30882176	SK-N-SH	brain:	n/a	chr22:30881538-30881559 chr22:30881546-30881556 chr22:30881545-30881558 chr22:30881544-30881560 chr22:30881512-30881521 chr22:30881543-30881561 chr22:30881549-30881558
8	CTCF	chr22:30881216-30881292	GM12891	blood:	n/a	n/a
9	CTCF	chr22:30881120-30881270	AG04449	skin:	n/a	n/a
10	RAD21	chr22:30881195-30881840	A549	lung:	n/a	chr22:30881541-30881560 chr22:30881543-30881555 chr22:30881545-30881555 chr22:30881544-30881557
11	CTCF	chr22:30881094-30881822	A549	lung:	n/a	chr22:30881538-30881559 chr22:30881546-30881556 chr22:30881545-30881558 chr22:30881544-30881560 chr22:30881512-30881521 chr22:30881543-30881561 chr22:30881549-30881558
12	RAD21	chr22:30881152-30881905	SK-N-SH	brain:	n/a	chr22:30881541-30881560 chr22:30881543-30881555 chr22:30881545-30881555 chr22:30881544-30881557
13	SMC3	chr22:30881136-30881908	SK-N-SH	brain:	n/a	chr22:30881545-30881555 chr22:30881545-30881559 chr22:30881551-30881559
14	CTCF	chr22:30881226-30881296	GM19239	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:30840899..30842135-chr22:30881081..30882272,7	MCF-7	breast:
2	chr22:30786734..30787783-chr22:30881073..30882029,10	K562	blood:
3	chr22:30840805..30841805-chr22:30881139..30882175,5	MCF-7	breast:
4	chr22:30786828..30787681-chr22:30881079..30881999,5	MCF-7	breast:
5	chr22:30786809..30787721-chr22:30881123..30882274,5	MCF-7	breast:
6	chr22:30651804..30652705-chr22:30881034..30881596,2	K562	blood:
7	chr22:30818688..30821603-chr22:30880263..30882823,2	MCF-7	breast:

Variant related genes	Relation type
SDC4P	TF binding region
ENSG00000242114	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1001409	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1008801	1.00[ASN][1000 genomes]
rs11912737	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13053262	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13053759	0.83[AMR][1000 genomes]
rs13054004	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13054381	0.82[AMR][1000 genomes]
rs13750	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16988720	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17670707	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17670808	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17738527	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17738540	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1859479	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1986969	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2023967	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2189835	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412989	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2412990	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35102600	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35530794	1.00[ASN][1000 genomes]
rs35841307	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4602314	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60308761	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6518693	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6518695	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7284873	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7285878	1.00[ASN][1000 genomes]
rs7286523	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7286807	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7287003	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7287135	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7287596	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7287943	0.93[EUR][1000 genomes]
rs7289277	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7289820	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7289828	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7291870	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7292573	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737942	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8136225	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8136992	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8137267	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8137718	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8138759	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8141108	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8141286	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8141318	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8141428	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8141671	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs886615	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs886616	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs886617	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9306262	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9606735	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9606736	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9606738	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9606739	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9606744	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9606745	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9606746	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9606747	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9606749	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9608935	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9608938	1.00[ASN][1000 genomes]
rs9608940	1.00[ASN][1000 genomes]
rs9608941	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9608942	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9608944	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9608946	0.96[EUR][1000 genomes]
rs9608955	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9608956	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9608960	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9608964	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9608966	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9608967	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9608968	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9608972	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][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	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9608936	SEC14L4	cis	lung	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30872800-30881400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr22:30874600-30894000	Weak transcription	Right Atrium	heart
3	chr22:30878000-30881800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr22:30879800-30882400	Enhancers	Gastric	stomach
5	chr22:30880000-30881600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr22:30880000-30881600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr22:30880600-30883400	Enhancers	Pancreas	Pancrea
8	chr22:30880800-30885600	Enhancers	Liver	Liver
9	chr22:30881200-30881600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr22:30881200-30881600	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr22:30881200-30881800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr22:30881200-30881800	Enhancers	Fetal Intestine Large	intestine
13	chr22:30881200-30881800	Enhancers	Osteobl	bone
14	chr22:30881200-30882000	Enhancers	Brain Hippocampus Middle	brain
15	chr22:30881200-30882000	Enhancers	Spleen	Spleen
16	chr22:30881200-30882000	Enhancers	Dnd41	blood

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