Variant report

Variant	rs240345
Chromosome Location	chr22:34058812-34058813
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:34052912..34055684-chr22:34057448..34059597,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133424	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs104860	0.85[EUR][1000 genomes]
rs13055437	0.89[ASN][1000 genomes]
rs19801	0.87[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs240328	0.90[EUR][1000 genomes]
rs240330	0.89[EUR][1000 genomes]
rs240332	0.90[EUR][1000 genomes]
rs240333	0.85[EUR][1000 genomes]
rs240335	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs240336	0.92[AMR][1000 genomes]
rs240337	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs240338	0.83[CEU][hapmap];0.87[CHB][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs240339	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs240340	0.83[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs240341	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs240342	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs240343	0.83[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs240344	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs240346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240347	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240348	0.83[CEU][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs240349	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240350	0.93[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240351	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240352	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240353	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240354	0.87[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240355	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240357	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs240358	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs240598	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs240599	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs240600	0.87[CHB][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs240601	0.87[CHB][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs240602	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs240603	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs240604	1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs240607	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs240608	0.96[CEU][hapmap]
rs80215	0.87[CHB][hapmap];0.83[JPT][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs80231	0.87[CHB][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes]
rs9621748	0.96[CEU][hapmap];0.87[CHB][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948523	chr22:33414164-34098417	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	nsv934109	chr22:33722066-34339500	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1062127	chr22:33755479-34085278	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv544683	chr22:33755479-34085278	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
5	nsv531588	chr22:33776857-34150188	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1055791	chr22:33822226-34159536	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	esv2763261	chr22:33831348-34288389	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
8	nsv917167	chr22:33852676-34137036	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1062832	chr22:33861531-34143295	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv544686	chr22:33861531-34143295	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1057450	chr22:33928913-34849012	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv914988	chr22:33975998-34083987	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv934161	chr22:33979015-34118621	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
14	nsv588935	chr22:34008430-34073758	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv914989	chr22:34011334-34083987	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs240345	CHEK2	cis	parietal	SCAN
rs240345	HMGXB4	cis	parietal	SCAN
rs240345	DEPDC5	cis	cerebellum	SCAN
rs240345	C22orf24	cis	cerebellum	SCAN
rs240345	TNR	trans	cerebellum	SCAN
rs240345	RASL10A	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:34003000-34062400	Weak transcription	Gastric	stomach
2	chr22:34044400-34062200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr22:34046600-34059400	Weak transcription	Primary B cells from peripheral blood	blood
4	chr22:34046800-34062200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr22:34050200-34062200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr22:34051000-34062200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr22:34052400-34063000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr22:34053400-34062200	Weak transcription	Fetal Brain Female	brain
9	chr22:34053800-34062200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr22:34053800-34064200	Weak transcription	Pancreas	Pancrea
11	chr22:34053800-34070400	Weak transcription	Lung	lung
12	chr22:34054200-34062400	Weak transcription	Psoas Muscle	Psoas
13	chr22:34055000-34062000	Weak transcription	Brain Angular Gyrus	brain
14	chr22:34055200-34068200	Weak transcription	Spleen	Spleen
15	chr22:34055800-34062400	Weak transcription	Fetal Muscle Leg	muscle
16	chr22:34056200-34062400	Weak transcription	Ovary	ovary
17	chr22:34056400-34060800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr22:34056400-34062400	Weak transcription	Fetal Stomach	stomach
19	chr22:34056600-34060800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr22:34056600-34061000	Weak transcription	Colon Smooth Muscle	Colon
21	chr22:34056600-34062000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr22:34056600-34062200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr22:34056600-34063000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr22:34056800-34062000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr22:34056800-34062000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr22:34056800-34062200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr22:34056800-34062200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr22:34056800-34062600	Weak transcription	Brain Substantia Nigra	brain
29	chr22:34057000-34062000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr22:34057600-34066200	Enhancers	Fetal Heart	heart
31	chr22:34057800-34062000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr22:34058200-34060000	Weak transcription	Fetal Brain Male	brain
33	chr22:34058400-34060000	Weak transcription	Brain Germinal Matrix	brain
34	chr22:34058400-34060000	Weak transcription	Right Atrium	heart
35	chr22:34058600-34059400	Weak transcription	Left Ventricle	heart
36	chr22:34058600-34059400	Weak transcription	Right Ventricle	heart
37	chr22:34058600-34061800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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