Variant report

Variant	rs4823003
Chromosome Location	chr22:29410232-29410233
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29405475..29407089-chr22:29407777..29410693,2	MCF-7	breast:
2	chr22:29404563..29408060-chr22:29409696..29411797,4	K562	blood:
3	chr22:29262470..29264565-chr22:29409487..29412264,2	K562	blood:
4	chr22:29382490..29384756-chr22:29408678..29411279,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183579	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs12484832	0.91[CEU][hapmap];0.82[JPT][hapmap]
rs132565	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17440734	0.96[CEU][hapmap];0.85[GIH][hapmap];0.89[TSI][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1883197	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1983553	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2064084	0.89[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2072774	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2347790	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs28541979	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4140643	0.96[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4404379	0.85[EUR][1000 genomes]
rs4580479	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs469994	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4820794	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4823002	0.93[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4823005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5762942	0.95[MKK][hapmap]
rs5997432	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5997433	1.00[CEU][hapmap];0.82[CHD][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs5997435	0.88[ASN][1000 genomes]
rs6005954	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6005955	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs6005956	0.96[CEU][hapmap]
rs6005958	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6005964	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6005965	0.96[CEU][hapmap];0.82[JPT][hapmap];0.88[YRI][hapmap];0.80[ASN][1000 genomes]
rs6005967	0.93[CEU][hapmap]
rs713834	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs727892	0.96[CEU][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap]
rs7290304	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs738246	0.92[CEU][hapmap]
rs8137254	0.96[CEU][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes]
rs8137499	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs874917	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9608719	0.93[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9608721	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9613771	0.81[EUR][1000 genomes]
rs9613776	0.96[CEU][hapmap]
rs9613777	0.96[CEU][hapmap]
rs9613784	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9613785	0.93[CEU][hapmap];0.82[JPT][hapmap]
rs964589	0.93[CEU][hapmap];0.80[EUR][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	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
2	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4823003	MN1	cis	cerebellum	SCAN
rs4823003	GAL3ST1	cis	cerebellum	SCAN
rs4823003	GGT5	cis	parietal	SCAN
rs4823003	SEZ6L	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29400600-29412000	Weak transcription	A549	lung
2	chr22:29400600-29425400	Weak transcription	NHEK	skin
3	chr22:29401200-29413400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr22:29401400-29414800	Weak transcription	Esophagus	oesophagus
5	chr22:29401400-29419200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr22:29401400-29425000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr22:29401800-29426200	Weak transcription	Colon Smooth Muscle	Colon
8	chr22:29402600-29412000	Weak transcription	Pancreas	Pancrea
9	chr22:29402800-29411400	Genic enhancers	HepG2	liver
10	chr22:29404800-29411000	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr22:29405200-29418000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr22:29405400-29410400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr22:29405400-29424600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr22:29406400-29410800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr22:29406600-29410800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr22:29407000-29410600	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr22:29407000-29411000	Enhancers	Fetal Intestine Large	intestine
18	chr22:29407000-29411000	Genic enhancers	Fetal Intestine Small	intestine
19	chr22:29407200-29410400	Enhancers	Psoas Muscle	Psoas
20	chr22:29407200-29411000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr22:29407400-29410400	Weak transcription	Lung	lung
22	chr22:29407800-29410600	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr22:29407800-29413400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr22:29408200-29410400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr22:29408200-29411600	Enhancers	Brain Anterior Caudate	brain
26	chr22:29408200-29412000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr22:29408200-29419400	Weak transcription	Fetal Stomach	stomach
28	chr22:29408200-29419400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr22:29408200-29422600	Weak transcription	Fetal Muscle Trunk	muscle
30	chr22:29408400-29410400	Weak transcription	Brain Hippocampus Middle	brain
31	chr22:29408400-29410400	Weak transcription	Left Ventricle	heart
32	chr22:29408400-29411400	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr22:29408400-29412200	Weak transcription	Gastric	stomach
34	chr22:29408600-29410800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr22:29408600-29411000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr22:29408600-29412200	Weak transcription	Stomach Mucosa	stomach
37	chr22:29408600-29419400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr22:29408600-29419400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr22:29408800-29410400	Weak transcription	Liver	Liver
40	chr22:29409200-29412200	Weak transcription	Fetal Brain Female	brain
41	chr22:29409200-29412200	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr22:29409200-29414800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr22:29409400-29414800	Weak transcription	Aorta	Aorta
44	chr22:29409600-29412200	Weak transcription	Small Intestine	intestine
45	chr22:29409600-29413800	Weak transcription	Fetal Lung	lung
46	chr22:29409800-29410800	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr22:29409800-29412600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr22:29410000-29410400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr22:29410000-29410400	Enhancers	Right Atrium	heart
50	chr22:29410000-29410800	Enhancers	Fetal Heart	heart

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