Variant report

Variant	rs10898989
Chromosome Location	chr11:74157393-74157394
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:74153484..74156082-chr11:74157168..74159879,2	K562	blood:
2	chr11:74152449..74154476-chr11:74156182..74158216,2	MCF-7	breast:
3	chr11:74155193..74158108-chr11:74170672..74173551,2	K562	blood:
4	chr11:74153867..74156607-chr11:74157168..74160666,3	K562	blood:

Variant related genes	Relation type
ENSG00000175538	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10793084	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs10793085	0.95[CHB][hapmap];0.84[CHD][hapmap];0.83[ASN][1000 genomes]
rs10898988	0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs11236106	0.83[ASN][1000 genomes]
rs12274367	0.83[ASN][1000 genomes]
rs12281178	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3132849	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3862800	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs484447	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs515589	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs517303	0.82[ASN][1000 genomes]
rs520837	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs537637	0.97[ASN][1000 genomes]
rs538805	0.81[ASN][1000 genomes]
rs539343	0.95[CHB][hapmap];0.82[CHD][hapmap];0.83[ASN][1000 genomes]
rs540279	0.83[ASN][1000 genomes]
rs544747	0.81[ASN][1000 genomes]
rs563722	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs56373920	0.83[ASN][1000 genomes]
rs591372	0.83[ASN][1000 genomes]
rs603502	0.82[ASN][1000 genomes]
rs612040	0.81[ASN][1000 genomes]
rs612700	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs615593	0.81[ASN][1000 genomes]
rs618993	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61901485	0.83[ASN][1000 genomes]
rs621109	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs621857	0.81[ASN][1000 genomes]
rs633568	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs638656	0.82[ASN][1000 genomes]
rs640500	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs642033	0.90[CHB][hapmap]
rs645184	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.87[JPT][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs658950	0.82[ASN][1000 genomes]
rs670722	0.81[ASN][1000 genomes]
rs670829	0.82[ASN][1000 genomes]
rs671946	0.82[ASN][1000 genomes]
rs684028	0.83[ASN][1000 genomes]
rs685684	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs692809	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs693884	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs694638	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7925353	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs7947671	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	esv34979	chr11:73878688-74533452	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv825994	chr11:73936667-74534455	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
6	nsv555443	chr11:74109166-74180489	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1041154	chr11:74114801-74177909	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv393	chr11:74135862-74181417	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv832209	chr11:74155883-74329119	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10898989	PGM2L1	cis	parietal	SCAN
rs10898989	INTS4	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74138800-74161600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:74153600-74158400	Enhancers	Fetal Muscle Leg	muscle
3	chr11:74154400-74160200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr11:74154400-74167600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr11:74154600-74167400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr11:74154600-74167800	Weak transcription	Liver	Liver
7	chr11:74154800-74158800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr11:74154800-74160200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr11:74154800-74160200	Weak transcription	Hela-S3	cervix
10	chr11:74154800-74171600	Weak transcription	Fetal Kidney	kidney
11	chr11:74155000-74167400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr11:74155200-74171200	Weak transcription	Right Atrium	heart
13	chr11:74155600-74160400	Weak transcription	Colon Smooth Muscle	Colon
14	chr11:74155600-74163400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr11:74155600-74167400	Weak transcription	Fetal Intestine Large	intestine
16	chr11:74155600-74169400	Weak transcription	Stomach Mucosa	stomach
17	chr11:74155800-74159600	Weak transcription	Fetal Thymus	thymus
18	chr11:74155800-74160000	Weak transcription	A549	lung
19	chr11:74155800-74160200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr11:74155800-74166800	Weak transcription	Fetal Intestine Small	intestine
21	chr11:74155800-74167600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr11:74156200-74160200	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr11:74156200-74167400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr11:74156200-74167800	Weak transcription	Ovary	ovary
25	chr11:74156400-74159200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr11:74156600-74160200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr11:74156600-74171400	Weak transcription	Psoas Muscle	Psoas
28	chr11:74156800-74160200	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr11:74157000-74159800	Weak transcription	Primary neutrophils fromperipheralblood	blood

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