Variant report

Variant	rs1365494
Chromosome Location	chr4:100806252-100806253
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:100805330..100807744-chr4:100813899..100815968,2	MCF-7	breast:
2	chr4:100732582..100733619-chr4:100805780..100806859,8	MCF-7	breast:
3	chr4:100481981..100482910-chr4:100806003..100806582,2	K562	blood:
4	chr4:100645156..100645805-chr4:100806019..100806629,2	MCF-7	breast:
5	chr4:100729667..100733158-chr4:100802564..100806778,3	MCF-7	breast:
6	chr4:100799869..100822436-chr4:100866015..100873106,54	K562	blood:
7	chr4:100732607..100733396-chr4:100806148..100806909,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109270	Chromatin interaction
ENSG00000245322	Chromatin interaction
ENSG00000164031	Chromatin interaction
ENSG00000164032	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10001730	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10002820	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10014424	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10016741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10018937	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10461176	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17029542	1.00[JPT][hapmap]
rs17029575	0.85[ASN][1000 genomes]
rs17029577	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17029592	0.83[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17029594	0.83[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17029601	0.88[YRI][hapmap];0.89[AFR][1000 genomes]
rs17029606	1.00[ASW][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs17029641	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs17029667	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17029681	0.90[ASN][1000 genomes]
rs17029696	1.00[ASW][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs17029698	1.00[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs17029717	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2282587	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2298734	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs28375729	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28445732	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs28497573	0.84[AFR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28553972	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs28561548	1.00[ASW][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs28566137	1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs28604943	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28635099	1.00[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2866175	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28705829	0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs28709045	1.00[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs28824275	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28893880	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3737485	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3775510	0.96[ASN][1000 genomes]
rs4463078	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs56996205	0.83[ASN][1000 genomes]
rs57001633	0.83[ASN][1000 genomes]
rs57238114	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs57862852	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs58512740	0.85[ASN][1000 genomes]
rs58699064	0.82[ASN][1000 genomes]
rs59439986	0.86[ASN][1000 genomes]
rs59768994	0.97[ASN][1000 genomes]
rs60203069	0.97[ASN][1000 genomes]
rs60584294	0.85[ASN][1000 genomes]
rs60899666	0.85[ASN][1000 genomes]
rs60994806	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs61229555	0.90[ASN][1000 genomes]
rs62305048	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:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879661	chr4:100805207-100869635	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1365494	BANK1	cis	cerebellum	SCAN
rs1365494	NFKB1	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100789600-100814200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr4:100790400-100814600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr4:100797000-100809600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr4:100797600-100809000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr4:100797800-100808400	Strong transcription	Adipose Nuclei	Adipose
6	chr4:100798000-100808200	Strong transcription	Liver	Liver
7	chr4:100798000-100809600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr4:100798000-100810800	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr4:100798200-100808400	Strong transcription	Placenta	Placenta
10	chr4:100798400-100806400	Strong transcription	HSMM	muscle
11	chr4:100798400-100814200	Weak transcription	Stomach Mucosa	stomach
12	chr4:100798600-100807600	Strong transcription	Duodenum Mucosa	Duodenum
13	chr4:100798600-100809000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:100798800-100808400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr4:100799000-100806600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:100799000-100806600	Strong transcription	Osteobl	bone
17	chr4:100799000-100808200	Strong transcription	NHDF-Ad	bronchial
18	chr4:100799000-100813400	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr4:100799200-100807200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr4:100799200-100808400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:100799200-100808400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr4:100799200-100811000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr4:100799400-100812200	Weak transcription	HepG2	liver
24	chr4:100799600-100808200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr4:100799600-100814800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:100799800-100806600	Strong transcription	Muscle Satellite Cultured Cells	--
27	chr4:100799800-100808200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr4:100800000-100810400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr4:100800200-100814200	Weak transcription	Hela-S3	cervix
30	chr4:100800600-100808200	Strong transcription	HUVEC	blood vessel
31	chr4:100801400-100809000	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr4:100801800-100814400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr4:100801800-100814600	Weak transcription	Psoas Muscle	Psoas
34	chr4:100802000-100809000	Weak transcription	Gastric	stomach
35	chr4:100802000-100812200	Weak transcription	Brain Angular Gyrus	brain
36	chr4:100802000-100814200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr4:100802000-100814200	Weak transcription	Aorta	Aorta
38	chr4:100802000-100814200	Weak transcription	Brain Germinal Matrix	brain
39	chr4:100802000-100814200	Weak transcription	Spleen	Spleen
40	chr4:100802000-100814200	Weak transcription	NHLF	lung
41	chr4:100802000-100814400	Weak transcription	Pancreas	Pancrea
42	chr4:100802200-100810000	Weak transcription	Fetal Intestine Small	intestine
43	chr4:100802200-100812800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr4:100802200-100814000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr4:100802200-100814200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr4:100802200-100814200	Weak transcription	Colonic Mucosa	Colon
47	chr4:100802200-100814200	Weak transcription	A549	lung
48	chr4:100802200-100814600	Weak transcription	Fetal Stomach	stomach
49	chr4:100802200-100814800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr4:100802200-100814800	Weak transcription	Esophagus	oesophagus

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