Variant report

Variant	rs739196
Chromosome Location	chr22:29311271-29311272
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29280624..29284164-chr22:29307760..29311501,3	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1222	0.94[CEU][hapmap];0.83[TSI][hapmap]
rs13053879	0.83[AFR][1000 genomes]
rs13056243	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13058031	0.94[CEU][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs13058453	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs132534	0.84[CHD][hapmap]
rs132539	0.89[CHD][hapmap]
rs16986825	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16986838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16986861	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16986864	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17514713	1.00[YRI][hapmap]
rs2267131	0.94[CEU][hapmap]
rs2301428	0.94[CEU][hapmap]
rs2347448	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs28360615	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34206997	0.83[AFR][1000 genomes]
rs34578331	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35050306	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs35814864	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs4055	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5752797	0.89[CEU][hapmap]
rs5752803	0.94[CEU][hapmap]
rs5752811	0.94[CEU][hapmap];0.84[TSI][hapmap]
rs5752816	0.83[AFR][1000 genomes]
rs5762767	0.88[CEU][hapmap];0.84[TSI][hapmap]
rs5762780	0.87[CEU][hapmap]
rs5762799	0.89[CEU][hapmap]
rs5762814	0.94[CEU][hapmap];0.84[TSI][hapmap]
rs5762816	0.94[CEU][hapmap];0.84[TSI][hapmap]
rs5762848	1.00[YRI][hapmap]
rs5762857	0.83[AFR][1000 genomes]
rs59203761	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs59224170	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs60468718	0.83[AFR][1000 genomes]
rs73170679	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs7364229	0.81[ASN][1000 genomes]
rs916332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs739196	SUSD2	cis	parietal	SCAN
rs739196	MN1	cis	cerebellum	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29303800-29313200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr22:29304400-29312400	Weak transcription	Fetal Brain Female	brain
3	chr22:29304400-29312600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr22:29304600-29312600	Weak transcription	Fetal Brain Male	brain
5	chr22:29304600-29313000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr22:29304800-29313800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr22:29305000-29312600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr22:29305000-29313600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr22:29305600-29313600	Weak transcription	NHEK	skin
10	chr22:29307400-29313000	Weak transcription	Brain Substantia Nigra	brain
11	chr22:29307600-29312600	Weak transcription	Brain Angular Gyrus	brain
12	chr22:29307800-29312200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr22:29308000-29312200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr22:29308000-29312400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr22:29308000-29312600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr22:29308000-29312600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr22:29308000-29312600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr22:29308000-29313000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr22:29308000-29313000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr22:29308000-29313000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr22:29308000-29313200	Weak transcription	Gastric	stomach
22	chr22:29308200-29311800	Weak transcription	Ovary	ovary
23	chr22:29308200-29312800	Weak transcription	Right Ventricle	heart
24	chr22:29308200-29313800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr22:29308200-29313800	Weak transcription	NH-A	brain
26	chr22:29308400-29311800	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr22:29308400-29312200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr22:29308400-29312200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr22:29308400-29312400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr22:29308400-29312400	Weak transcription	Fetal Stomach	stomach
31	chr22:29308400-29312600	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr22:29308400-29312800	Weak transcription	Brain Germinal Matrix	brain
33	chr22:29308400-29312800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr22:29308400-29313000	Weak transcription	HSMM	muscle
35	chr22:29308400-29313200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr22:29308400-29313200	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr22:29308400-29313200	Weak transcription	Stomach Mucosa	stomach
38	chr22:29308600-29311400	Weak transcription	Fetal Kidney	kidney
39	chr22:29308600-29312000	Weak transcription	Left Ventricle	heart
40	chr22:29308600-29312200	Weak transcription	Fetal Muscle Leg	muscle
41	chr22:29308600-29312200	Weak transcription	Small Intestine	intestine
42	chr22:29308600-29312400	Weak transcription	Fetal Heart	heart
43	chr22:29308600-29312600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr22:29308600-29312600	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr22:29308600-29312800	Weak transcription	HSMMtube	muscle
46	chr22:29308600-29313000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr22:29308600-29313000	Weak transcription	Right Atrium	heart
48	chr22:29308600-29314000	Weak transcription	Adipose Nuclei	Adipose
49	chr22:29308600-29314000	Weak transcription	NHLF	lung
50	chr22:29309200-29312000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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