Variant report

Variant	rs404445
Chromosome Location	chr4:48350757-48350758
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48350227..48353162-chr4:48356080..48357994,2	K562	blood:
2	chr4:48349775..48352299-chr4:48353081..48355903,3	K562	blood:
3	chr4:48342295..48345695-chr4:48348596..48352687,7	MCF-7	breast:
4	chr4:48342958..48345732-chr4:48348835..48351792,2	MCF-7	breast:
5	chr4:48337400..48346343-chr4:48347805..48355704,14	K562	blood:
6	chr4:48328527..48330606-chr4:48349745..48351670,2	K562	blood:
7	chr4:48346882..48348699-chr4:48349922..48352007,2	K562	blood:

Variant related genes	Relation type
ENSG00000109171	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10003230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10026398	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10029785	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1055721	0.90[YRI][hapmap]
rs10938534	0.81[JPT][hapmap]
rs1117010	0.81[ASN][1000 genomes]
rs11945562	0.86[JPT][hapmap]
rs12507206	0.80[ASN][1000 genomes]
rs12511991	0.80[ASN][1000 genomes]
rs12645501	0.81[JPT][hapmap]
rs12645951	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12649527	0.81[ASN][1000 genomes]
rs12649528	0.81[ASN][1000 genomes]
rs13105385	0.81[ASN][1000 genomes]
rs13115295	0.80[ASN][1000 genomes]
rs1352433	0.81[ASN][1000 genomes]
rs1472967	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1586540	0.81[ASN][1000 genomes]
rs1703973	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1948167	0.81[ASN][1000 genomes]
rs2029348	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2291474	0.83[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2291475	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2353312	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35758434	0.81[ASN][1000 genomes]
rs372825	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs382335	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3828496	0.81[ASN][1000 genomes]
rs392187	0.83[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs403495	0.88[ASN][1000 genomes]
rs404348	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs404656	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs411261	0.89[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs421336	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs421833	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs429969	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs432927	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs445892	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs449376	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs450498	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4694895	0.81[ASN][1000 genomes]
rs62309425	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6447634	0.81[ASN][1000 genomes]
rs6447635	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6811148	0.81[JPT][hapmap]
rs6816010	1.00[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6816352	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6821277	0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6829705	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6829716	0.86[JPT][hapmap]
rs6836010	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6836632	0.86[JPT][hapmap]
rs6837335	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6844211	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6848073	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6848395	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7438704	0.81[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7654770	0.86[JPT][hapmap]
rs7664981	0.94[YRI][hapmap]
rs7668529	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7672892	0.82[ASN][1000 genomes]
rs7674269	0.80[ASN][1000 genomes]
rs7678164	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7678379	0.86[JPT][hapmap]
rs7683398	0.81[JPT][hapmap]
rs7697851	0.86[JPT][hapmap]
rs7700018	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs923372	0.81[ASN][1000 genomes]
rs923373	0.81[ASN][1000 genomes]
rs9291323	0.82[ASN][1000 genomes]
rs937888	0.81[JPT][hapmap]
rs952289	0.81[JPT][hapmap]
rs974014	0.81[ASN][1000 genomes]
rs974015	0.81[ASN][1000 genomes]
rs974016	0.80[ASN][1000 genomes]
rs992423	0.86[JPT][hapmap]
rs9996532	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[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	nsv1006610	chr4:48209294-48415387	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv537085	chr4:48209294-48415387	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs404445	SLAIN2	cis	parietal	SCAN
rs404445	OCIAD2	cis	cerebellum	SCAN
rs404445	SLAIN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48344800-48352200	Weak transcription	Pancreas	Pancrea
2	chr4:48344800-48354400	Weak transcription	Esophagus	oesophagus
3	chr4:48344800-48362400	Weak transcription	Gastric	stomach
4	chr4:48345800-48353600	Weak transcription	Spleen	Spleen
5	chr4:48345800-48356000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr4:48345800-48356600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr4:48346000-48350800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:48346000-48351200	Weak transcription	A549	lung
9	chr4:48346000-48353000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
10	chr4:48346000-48362800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr4:48346200-48352200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr4:48346200-48354600	Weak transcription	Fetal Intestine Small	intestine
13	chr4:48346200-48356200	Weak transcription	Fetal Thymus	thymus
14	chr4:48346200-48356600	Weak transcription	HUVEC	blood vessel
15	chr4:48346200-48358400	Weak transcription	Small Intestine	intestine
16	chr4:48346200-48362400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:48346400-48361200	Weak transcription	Thymus	Thymus
18	chr4:48346600-48354800	Weak transcription	Primary B cells from cord blood	blood
19	chr4:48346600-48371000	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr4:48347000-48352200	Enhancers	Primary T cells from cord blood	blood
21	chr4:48347000-48354600	Weak transcription	Aorta	Aorta
22	chr4:48347200-48359600	Weak transcription	Fetal Stomach	stomach
23	chr4:48347400-48350800	Weak transcription	Fetal Brain Male	brain
24	chr4:48347400-48352200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr4:48347400-48353600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr4:48347400-48353800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr4:48347400-48354600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:48347400-48362200	Weak transcription	Brain Substantia Nigra	brain
29	chr4:48347400-48362200	Weak transcription	NHLF	lung
30	chr4:48347600-48351200	Weak transcription	Brain Angular Gyrus	brain
31	chr4:48347600-48351800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr4:48347600-48351800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr4:48347600-48352800	Weak transcription	Fetal Kidney	kidney
34	chr4:48347600-48353000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr4:48347600-48354600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr4:48347600-48365000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr4:48348200-48350800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr4:48348200-48353600	Weak transcription	Dnd41	blood
39	chr4:48348400-48352000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr4:48348600-48350800	Weak transcription	HepG2	liver
41	chr4:48348600-48351000	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr4:48348600-48353000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr4:48348600-48353400	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr4:48348600-48362400	Weak transcription	Fetal Lung	lung
45	chr4:48348800-48355800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr4:48348800-48358200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr4:48348800-48363000	Weak transcription	Hela-S3	cervix
48	chr4:48348800-48371000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr4:48349000-48350800	Weak transcription	Fetal Brain Female	brain
50	chr4:48349000-48356600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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