Variant report

Variant	rs17440734
Chromosome Location	chr22:29409966-29409967
allele	C/T
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: 56 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs12484832	0.96[CEU][hapmap]
rs12485244	0.96[ASN][1000 genomes]
rs132565	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1977047	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1983553	0.96[CEU][hapmap];0.80[YRI][hapmap]
rs2064084	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2072774	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2103544	0.97[ASN][1000 genomes]
rs2347789	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2347790	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4140643	0.92[CEU][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4333023	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4404379	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4580479	0.83[EUR][1000 genomes]
rs4594553	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4616575	0.97[ASN][1000 genomes]
rs469994	1.00[CEU][hapmap];0.81[YRI][hapmap];0.91[EUR][1000 genomes]
rs4820794	0.92[CEU][hapmap]
rs4823002	0.96[CEU][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4823003	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]
rs4823005	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5997430	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5997431	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5997432	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5997433	0.96[CEU][hapmap]
rs5997434	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6005954	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6005955	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6005956	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6005958	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6005959	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6005964	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005965	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6005967	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.94[ASN][1000 genomes]
rs713834	0.96[CEU][hapmap]
rs727892	1.00[CEU][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap]
rs7284304	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7287517	0.95[ASN][1000 genomes]
rs7290304	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]
rs738246	0.96[CEU][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.87[MEX][hapmap]
rs8137254	0.92[CEU][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs8137499	1.00[CEU][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8142591	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs874915	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs874916	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs874917	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9608719	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs9613768	0.89[CHD][hapmap]
rs9613771	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9613776	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9613777	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9613782	0.87[CHD][hapmap]
rs9613785	0.96[CEU][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap]
rs964589	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][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
rs17440734	MN1	cis	cerebellum	SCAN
rs17440734	SEZ6L	cis	cerebellum	SCAN
rs17440734	GGT5	cis	parietal	SCAN
rs17440734	GAL3ST1	cis	cerebellum	SCAN

Chromatin state (count:64 , 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	chr22:29405400-29410200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr22:29405400-29410400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr22:29405400-29424600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr22:29406400-29410800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr22:29406600-29410800	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr22:29407000-29410600	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr22:29407000-29411000	Enhancers	Fetal Intestine Large	intestine
19	chr22:29407000-29411000	Genic enhancers	Fetal Intestine Small	intestine
20	chr22:29407200-29410400	Enhancers	Psoas Muscle	Psoas
21	chr22:29407200-29411000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr22:29407400-29410400	Weak transcription	Lung	lung
23	chr22:29407800-29410000	Weak transcription	Brain Substantia Nigra	brain
24	chr22:29407800-29410600	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr22:29407800-29413400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr22:29408000-29410000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr22:29408000-29410200	Weak transcription	Right Ventricle	heart
28	chr22:29408200-29410400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr22:29408200-29411600	Enhancers	Brain Anterior Caudate	brain
30	chr22:29408200-29412000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr22:29408200-29419400	Weak transcription	Fetal Stomach	stomach
32	chr22:29408200-29419400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr22:29408200-29422600	Weak transcription	Fetal Muscle Trunk	muscle
34	chr22:29408400-29410000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr22:29408400-29410000	Weak transcription	Fetal Heart	heart
36	chr22:29408400-29410000	Weak transcription	Fetal Kidney	kidney
37	chr22:29408400-29410200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr22:29408400-29410400	Weak transcription	Brain Hippocampus Middle	brain
39	chr22:29408400-29410400	Weak transcription	Left Ventricle	heart
40	chr22:29408400-29411400	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr22:29408400-29412200	Weak transcription	Gastric	stomach
42	chr22:29408600-29410000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr22:29408600-29410200	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr22:29408600-29410800	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr22:29408600-29411000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr22:29408600-29412200	Weak transcription	Stomach Mucosa	stomach
47	chr22:29408600-29419400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr22:29408600-29419400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr22:29408800-29410400	Weak transcription	Liver	Liver
50	chr22:29409000-29410000	Weak transcription	Right Atrium	heart

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