Variant report

Variant	rs6005867
Chromosome Location	chr22:29165120-29165121
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	SRF	chr22:29165081-29165494	H1-hESC	embryonic stem cell:	n/a	chr22:29165295-29165313
2	SP1	chr22:29164851-29165362	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAFK	chr22:29165113-29165316	HepG2	liver:	n/a	n/a
4	NFYB	chr22:29165003-29165539	K562	blood:	n/a	chr22:29165197-29165212 chr22:29165172-29165187 chr22:29165245-29165260 chr22:29165221-29165236
5	NFYA	chr22:29165040-29165448	Hela-S3	cervix:	n/a	chr22:29165224-29165242 chr22:29165248-29165266 chr22:29165200-29165218
6	SRF	chr22:29165052-29165536	H1-hESC	embryonic stem cell:	n/a	chr22:29165295-29165313
7	SP1	chr22:29165010-29165314	GM12878	blood:	n/a	n/a
8	MAFF	chr22:29165114-29165305	HepG2	liver:	n/a	n/a
9	NFYB	chr22:29164913-29165474	Hela-S3	cervix:	n/a	chr22:29165197-29165212 chr22:29165172-29165187 chr22:29165245-29165260 chr22:29165221-29165236
10	NFYB	chr22:29164997-29165594	GM12878	blood:	n/a	chr22:29165197-29165212 chr22:29165172-29165187 chr22:29165245-29165260 chr22:29165221-29165236
11	SP1	chr22:29164982-29165358	GM12878	blood:	n/a	n/a
12	SETDB1	chr22:29164781-29165561	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:29164518..29166292-chr22:29215765..29218524,2	MCF-7	breast:
2	chr22:29163517..29166868-chr22:29167039..29168960,4	K562	blood:
3	chr22:29136893..29139522-chr22:29164321..29165928,2	MCF-7	breast:
4	chr22:29134226..29139597-chr22:29164663..29170736,9	K562	blood:
5	chr22:29160228..29162421-chr22:29163299..29165461,2	MCF-7	breast:

Variant related genes	Relation type
CCDC117	TF binding region
ENSG00000183765	Chromatin interaction
ENSG00000159873	Chromatin interaction
ENSG00000100209	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs12628211	0.94[ASN][1000 genomes]
rs2097461	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2239815	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2269577	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2347447	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2881635	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35259224	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3788409	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5752795	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752798	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752801	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs5752804	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5752807	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5752809	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5752812	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5752813	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5762784	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5762788	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5762795	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762803	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs5762815	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5762824	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5762825	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5762853	0.83[ASN][1000 genomes]
rs5762854	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5762863	0.84[ASN][1000 genomes]
rs5762864	0.84[ASN][1000 genomes]
rs5997408	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005869	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6005872	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6005881	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6005892	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6005916	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6005927	0.81[ASN][1000 genomes]
rs6005929	0.83[ASN][1000 genomes]
rs7287124	0.94[ASN][1000 genomes]
rs7287806	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs763073	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8137969	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9625566	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9625588	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv9895	chr22:29029961-29184277	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	nsv834169	chr22:29095446-29303929	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6005867	XBP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29145800-29168000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr22:29148000-29167000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr22:29149600-29165400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr22:29154400-29167400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr22:29164400-29166000	Enhancers	HepG2	liver
6	chr22:29164800-29167200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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