Variant report

Variant	rs16986825
Chromosome Location	chr22:29300306-29300307
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29195884..29197508-chr22:29298766..29301210,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226471	Chromatin interaction
ENSG00000100219	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1222	0.94[CEU][hapmap];0.83[TSI][hapmap]
rs13056243	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13058031	0.94[CEU][hapmap];0.90[MKK][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs13058453	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs132534	0.84[CHD][hapmap]
rs132539	0.89[CHD][hapmap]
rs16986838	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][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]
rs16986861	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16986864	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17514713	1.00[YRI][hapmap]
rs2267131	0.94[CEU][hapmap]
rs2301428	0.94[CEU][hapmap]
rs2347448	0.82[EUR][1000 genomes]
rs28360615	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34578331	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35050306	0.82[EUR][1000 genomes]
rs35814864	0.82[EUR][1000 genomes]
rs4055	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs5752797	0.89[CEU][hapmap]
rs5752803	0.94[CEU][hapmap]
rs5752811	0.94[CEU][hapmap];0.84[TSI][hapmap]
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]
rs59203761	0.83[EUR][1000 genomes]
rs59224170	0.83[EUR][1000 genomes]
rs73170679	0.82[EUR][1000 genomes]
rs739196	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]
rs916332	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv834169	chr22:29095446-29303929	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	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

Variant related diseases (count:1)

Disease	PMID	Source
Pancreatic cancer	25086665	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16986825	MN1	cis	cerebellum	SCAN
rs16986825	SUSD2	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29288000-29301800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr22:29291200-29300600	Weak transcription	Psoas Muscle	Psoas
3	chr22:29292400-29300600	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr22:29295600-29300600	Weak transcription	Brain Substantia Nigra	brain
5	chr22:29296200-29300400	Weak transcription	HSMMtube	muscle
6	chr22:29296400-29300400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr22:29296600-29300400	Weak transcription	HSMM	muscle
8	chr22:29296800-29310200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr22:29297400-29300600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr22:29298200-29301000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr22:29298400-29301200	Enhancers	Adipose Nuclei	Adipose
12	chr22:29298400-29301200	Enhancers	Fetal Muscle Leg	muscle
13	chr22:29298400-29301400	Enhancers	Right Ventricle	heart
14	chr22:29298400-29302800	Enhancers	Liver	Liver
15	chr22:29298400-29308400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr22:29298400-29310400	Enhancers	Fetal Intestine Large	intestine
17	chr22:29298600-29300800	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr22:29298600-29300800	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr22:29298600-29300800	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr22:29298600-29301000	Enhancers	Duodenum Mucosa	Duodenum
21	chr22:29298600-29301200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr22:29298600-29302000	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr22:29298600-29302400	Enhancers	Placenta	Placenta
24	chr22:29298600-29302600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr22:29298600-29302600	Enhancers	Fetal Lung	lung
26	chr22:29298600-29302800	Enhancers	Fetal Kidney	kidney
27	chr22:29298600-29304600	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr22:29298600-29305000	Enhancers	Brain Anterior Caudate	brain
29	chr22:29298600-29305400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr22:29298800-29301000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr22:29298800-29301200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr22:29298800-29301200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr22:29298800-29301200	Enhancers	Fetal Heart	heart
34	chr22:29298800-29302000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr22:29298800-29302800	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr22:29298800-29302800	Enhancers	Rectal Smooth Muscle	rectum
37	chr22:29298800-29304400	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr22:29298800-29305200	Enhancers	Brain Cingulate Gyrus	brain
39	chr22:29299000-29300400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr22:29299000-29300600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
41	chr22:29299000-29300800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr22:29299000-29300800	Flanking Active TSS	Stomach Smooth Muscle	stomach
43	chr22:29299000-29301000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr22:29299000-29301200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr22:29299000-29301200	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr22:29299000-29301200	Enhancers	Left Ventricle	heart
47	chr22:29299000-29301400	Enhancers	Fetal Stomach	stomach
48	chr22:29299000-29301400	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr22:29299000-29301600	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr22:29299000-29301600	Enhancers	Aorta	Aorta

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