Variant report

Variant	rs11153171
Chromosome Location	chr6:109653825-109653826
allele	C/T
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	chr6:109653819-109653885	Hela-S3	cervix:	n/a	chr6:109653826-109653844
2	RAD21	chr6:109653619-109653984	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr6:109653760-109653910	HepG2	liver:	n/a	chr6:109653826-109653844
4	CTCF	chr6:109653740-109653890	MCF-7	breast:	n/a	chr6:109653826-109653844
5	CTCF	chr6:109653680-109653830	Hela-S3	cervix:	n/a	n/a
6	CTCF	chr6:109653804-109653871	HepG2	liver:	n/a	chr6:109653826-109653844
7	RAD21	chr6:109653744-109653929	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr6:109653778-109653924	MCF-7	breast:	n/a	chr6:109653826-109653844
9	CTCF	chr6:109653797-109653913	MCF-7	breast:	n/a	chr6:109653826-109653844
10	CTCF	chr6:109653819-109653911	MCF-7	breast:	n/a	chr6:109653826-109653844
11	CTCF	chr6:109653680-109653830	MCF-7	breast:	n/a	n/a
12	CTCF	chr6:109653812-109653918	MCF-7	breast:	n/a	chr6:109653826-109653844
13	CTCF	chr6:109653773-109653927	MCF-7	breast:	n/a	chr6:109653826-109653844
14	CTCF	chr6:109653800-109653950	HEK293	kidney:	n/a	chr6:109653826-109653844
15	CTCF	chr6:109653825-109653912	H1-hESC	embryonic stem cell:	n/a	chr6:109653826-109653844

No.	Distal block	Cell Line	Cell type
1	chr6:109649495..109651298-chr6:109651628..109654623,3	K562	blood:
2	chr6:109652681..109655937-chr6:109701274..109703936,3	MCF-7	breast:
3	chr6:109652928..109655072-chr6:109655937..109657890,2	MCF-7	breast:

Variant related genes	Relation type
RPL7P28	TF binding region
ENSG00000135535	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10080429	0.84[EUR][1000 genomes]
rs1040284	0.87[EUR][1000 genomes]
rs10457190	0.88[EUR][1000 genomes]
rs1048203	0.86[CEU][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs10782161	0.83[EUR][1000 genomes]
rs10782162	0.82[CEU][hapmap]
rs10872032	0.88[EUR][1000 genomes]
rs11153174	0.87[CEU][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes]
rs11153175	0.87[CEU][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes]
rs11153176	0.87[EUR][1000 genomes]
rs11153177	0.83[EUR][1000 genomes]
rs11153180	0.83[EUR][1000 genomes]
rs11153181	0.83[EUR][1000 genomes]
rs11251	0.87[CHB][hapmap]
rs11967108	0.87[CEU][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes]
rs12190920	0.86[CEU][hapmap]
rs12193493	0.87[EUR][1000 genomes]
rs12197114	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs12206928	0.85[EUR][1000 genomes]
rs12213313	0.83[EUR][1000 genomes]
rs12524273	0.86[EUR][1000 genomes]
rs12524639	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs12528822	0.86[CEU][hapmap];0.87[JPT][hapmap];0.89[EUR][1000 genomes]
rs13212766	0.84[EUR][1000 genomes]
rs1322816	0.86[EUR][1000 genomes]
rs1358997	0.86[EUR][1000 genomes]
rs1358998	0.86[CEU][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs1476387	0.87[CHB][hapmap]
rs1590306	0.87[EUR][1000 genomes]
rs17070580	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs1923725	0.87[CEU][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs2236582	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs2275650	0.86[CEU][hapmap];0.87[JPT][hapmap];0.88[EUR][1000 genomes]
rs2277113	0.87[CHB][hapmap]
rs34202013	0.87[EUR][1000 genomes]
rs35056702	0.84[EUR][1000 genomes]
rs36035949	0.86[EUR][1000 genomes]
rs36099706	0.83[EUR][1000 genomes]
rs3757234	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs3778474	0.87[CHB][hapmap]
rs3778475	0.87[EUR][1000 genomes]
rs3799839	0.86[EUR][1000 genomes]
rs3818934	0.88[EUR][1000 genomes]
rs4946967	0.87[CHB][hapmap]
rs59906308	0.82[EUR][1000 genomes]
rs6911838	0.91[CEU][hapmap];0.80[CHB][hapmap];0.81[EUR][1000 genomes]
rs6920962	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs6929023	0.86[EUR][1000 genomes]
rs7372	0.87[EUR][1000 genomes]
rs752262	0.82[JPT][hapmap]
rs7748669	0.87[CHB][hapmap]
rs7754650	0.87[CHB][hapmap]
rs7773095	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs910730	0.87[CHB][hapmap]
rs9320287	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs9480933	0.89[EUR][1000 genomes]
rs9480948	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs9480951	0.84[EUR][1000 genomes]
rs9480953	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs9480955	0.84[EUR][1000 genomes]
rs9480957	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs9487068	0.86[EUR][1000 genomes]
rs9487094	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs9487095	0.84[EUR][1000 genomes]
rs9487097	0.80[EUR][1000 genomes]
rs9487098	0.80[EUR][1000 genomes]
rs9487100	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs9885646	0.91[CEU][hapmap];0.84[EUR][1000 genomes]

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	nsv5435	chr6:109633035-109669127	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11153171	AKD1	cis	brain	BrainEAC
rs11153171	MICAL1	Cis_1M	lymphoblastoid	RTeQTL
rs11153171	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs11153171	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs11153171	SMPD2	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109629600-109654000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:109644600-109675200	Weak transcription	Primary T cells from cord blood	blood
3	chr6:109644800-109657400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:109645400-109662400	Weak transcription	Aorta	Aorta
5	chr6:109649200-109654000	Weak transcription	K562	blood
6	chr6:109651600-109654600	Enhancers	Stomach Mucosa	stomach
7	chr6:109653000-109655000	Enhancers	Fetal Intestine Large	intestine
8	chr6:109653000-109655000	Enhancers	Fetal Intestine Small	intestine
9	chr6:109653000-109655000	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr6:109653400-109654400	Enhancers	Duodenum Mucosa	Duodenum
11	chr6:109653400-109654400	Active TSS	Rectal Smooth Muscle	rectum
12	chr6:109653400-109654400	Enhancers	Right Ventricle	heart
13	chr6:109653400-109658800	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr6:109653600-109654000	Enhancers	Small Intestine	intestine
15	chr6:109653600-109654200	Enhancers	Primary B cells from peripheral blood	blood
16	chr6:109653600-109654200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr6:109653600-109654200	Enhancers	Spleen	Spleen
18	chr6:109653600-109654400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr6:109653600-109654400	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr6:109653600-109654600	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr6:109653600-109654600	Enhancers	HepG2	liver
22	chr6:109653800-109654000	Enhancers	Pancreas	Pancrea
23	chr6:109653800-109654200	Enhancers	Primary T cells fromperipheralblood	blood
24	chr6:109653800-109654200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:109653800-109654200	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr6:109653800-109654400	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr6:109653800-109654400	Enhancers	Esophagus	oesophagus
28	chr6:109653800-109654400	Enhancers	Gastric	stomach
29	chr6:109653800-109654400	Enhancers	Lung	lung
30	chr6:109653800-109654400	Enhancers	Hela-S3	cervix
31	chr6:109653800-109656400	Weak transcription	Colonic Mucosa	Colon

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