Variant report

Variant	rs5997898
Chromosome Location	chr22:31572963-31572964
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:31567568..31570876-chr22:31571538..31573620,3	MCF-7	breast:
2	chr22:31572111..31576977-chr22:31606424..31611296,5	MCF-7	breast:
3	chr22:31542052..31544583-chr22:31572423..31574953,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182541	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1034587	0.91[JPT][hapmap]
rs12166373	0.83[MEX][hapmap]
rs12627941	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs131209	0.83[MEX][hapmap]
rs131213	0.83[MEX][hapmap]
rs17220369	0.91[JPT][hapmap]
rs2027982	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2239905	0.91[JPT][hapmap]
rs2267169	0.87[JPT][hapmap]
rs2267171	0.91[JPT][hapmap]
rs2283878	0.91[JPT][hapmap]
rs2283880	0.87[JPT][hapmap]
rs2413041	0.91[JPT][hapmap]
rs28715	0.83[MEX][hapmap]
rs4561750	0.91[JPT][hapmap]
rs4615	0.91[JPT][hapmap]
rs4820041	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4820961	0.87[MEX][hapmap]
rs5749231	0.91[JPT][hapmap]
rs5749232	0.85[JPT][hapmap]
rs5749237	0.91[JPT][hapmap]
rs5749244	0.91[JPT][hapmap]
rs5749254	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs5753488	0.87[JPT][hapmap]
rs5753518	0.86[JPT][hapmap]
rs5753551	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs5753559	0.91[JPT][hapmap]
rs5753560	0.91[JPT][hapmap]
rs5994376	0.82[MEX][hapmap]
rs5997919	0.87[MEX][hapmap]
rs5997929	0.87[MEX][hapmap]
rs5997940	0.91[JPT][hapmap]
rs713947	0.87[MEX][hapmap]
rs7285171	0.87[MEX][hapmap]
rs7286648	0.87[MEX][hapmap]
rs7287402	0.87[MEX][hapmap]
rs737809	0.91[JPT][hapmap]
rs739427	0.83[MEX][hapmap]
rs886074	0.91[JPT][hapmap]
rs9609263	0.88[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap]

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	nsv459871	chr22:31551160-31680624	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	nsv588893	chr22:31551160-31680624	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
3	nsv1067003	chr22:31558663-31697093	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs5997898	DRG1	Cis_1M	lymphoblastoid	RTeQTL
rs5997898	MN1	cis	parietal	SCAN
rs5997898	RNF185	cis	cerebellum	SCAN
rs5997898	RHBDD3	cis	cerebellum	SCAN
rs5997898	PISD	cis	cerebellum	SCAN
rs5997898	CRYBB1	cis	cerebellum	SCAN
rs5997898	LIMK2	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31557000-31573000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr22:31557000-31575200	Weak transcription	Esophagus	oesophagus
3	chr22:31557200-31591200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr22:31557400-31575000	Weak transcription	Gastric	stomach
5	chr22:31557400-31579800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr22:31557400-31595200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr22:31557400-31597800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr22:31557600-31575000	Weak transcription	Colonic Mucosa	Colon
9	chr22:31557600-31578600	Weak transcription	K562	blood
10	chr22:31557600-31591800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr22:31557800-31587000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr22:31557800-31588400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr22:31558000-31578000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr22:31558200-31573000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr22:31558200-31575000	Weak transcription	Stomach Mucosa	stomach
16	chr22:31558400-31573000	Weak transcription	Fetal Heart	heart
17	chr22:31558600-31583000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr22:31558600-31591400	Weak transcription	Primary hematopoietic stem cells	blood
19	chr22:31558800-31591200	Weak transcription	Fetal Brain Male	brain
20	chr22:31558800-31606000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr22:31559600-31575000	Weak transcription	Pancreas	Pancrea
22	chr22:31562000-31573000	Weak transcription	Fetal Brain Female	brain
23	chr22:31562000-31573200	Weak transcription	HepG2	liver
24	chr22:31562000-31575600	Weak transcription	Fetal Kidney	kidney
25	chr22:31562400-31583200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr22:31562600-31578400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr22:31563000-31577400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr22:31563800-31574000	Weak transcription	Fetal Muscle Leg	muscle
29	chr22:31564200-31573000	Weak transcription	Fetal Intestine Large	intestine
30	chr22:31564600-31574400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr22:31564600-31575400	Weak transcription	Dnd41	blood
32	chr22:31564600-31582600	Weak transcription	Fetal Thymus	thymus
33	chr22:31566200-31583000	Weak transcription	Brain Angular Gyrus	brain
34	chr22:31566400-31575200	Weak transcription	Right Atrium	heart
35	chr22:31566400-31575600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr22:31566400-31583000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr22:31566800-31573000	Weak transcription	Right Ventricle	heart
38	chr22:31566800-31575200	Weak transcription	Left Ventricle	heart
39	chr22:31567000-31575400	Weak transcription	Spleen	Spleen
40	chr22:31569200-31573000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr22:31569600-31573000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr22:31569600-31573400	Weak transcription	A549	lung
43	chr22:31569600-31573600	Weak transcription	Lung	lung
44	chr22:31569600-31575000	Weak transcription	Psoas Muscle	Psoas
45	chr22:31569600-31583200	Weak transcription	Brain Anterior Caudate	brain
46	chr22:31569800-31575400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr22:31569800-31575600	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr22:31569800-31583000	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr22:31569800-31591600	Weak transcription	Small Intestine	intestine
50	chr22:31570000-31573200	Weak transcription	Adipose Nuclei	Adipose

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