Variant report

Variant	rs10516411
Chromosome Location	chr4:22437930-22437931
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	chr4:22435935..22438268-chr4:22516437..22518541,2	MCF-7	breast:
2	chr4:22437735..22439383-chr4:22516765..22518580,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152990	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10003859	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs10003883	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs13109198	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13110697	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13129189	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs13139516	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13145061	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13148867	1.00[ASW][hapmap]
rs13152378	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16872682	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16872686	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2126633	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2323523	1.00[ASW][hapmap]
rs28437151	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28726245	0.85[CHB][hapmap];0.96[CHD][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs28736882	0.82[ASN][1000 genomes]
rs34228241	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35426712	0.91[EUR][1000 genomes]
rs35852147	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35926750	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36111920	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4697013	0.87[EUR][1000 genomes]
rs4697298	1.00[ASW][hapmap]
rs4697300	0.85[CHB][hapmap];0.96[CHD][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs4697301	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4697306	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57133360	0.91[EUR][1000 genomes]
rs59022936	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60379399	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61744997	0.91[EUR][1000 genomes]
rs71608917	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs716411	0.91[EUR][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	esv3349061	chr4:22379581-22887563	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv878752	chr4:22414023-22501043	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv821634	chr4:22427074-22865948	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10516411	KBTBD12	trans	lymphoblastoid	seeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:22371600-22449800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:22383200-22438000	Weak transcription	Lung	lung
3	chr4:22383600-22442800	Weak transcription	A549	lung
4	chr4:22386000-22446600	Weak transcription	Fetal Thymus	thymus
5	chr4:22388200-22442800	Weak transcription	Brain Germinal Matrix	brain
6	chr4:22388400-22473600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr4:22388800-22469600	Weak transcription	Colonic Mucosa	Colon
8	chr4:22389200-22473600	Weak transcription	Fetal Brain Male	brain
9	chr4:22390600-22439600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr4:22390600-22456200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr4:22390600-22459800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr4:22393400-22444800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr4:22393600-22459800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr4:22393800-22446400	Weak transcription	NH-A	brain
15	chr4:22393800-22453000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr4:22399800-22442800	Weak transcription	Fetal Brain Female	brain
17	chr4:22400000-22448000	Weak transcription	Left Ventricle	heart
18	chr4:22400800-22449600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:22400800-22461800	Weak transcription	Gastric	stomach
20	chr4:22405400-22446000	Weak transcription	Pancreas	Pancrea
21	chr4:22412800-22446000	Weak transcription	Thymus	Thymus
22	chr4:22416800-22449600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:22417600-22442200	Weak transcription	Hela-S3	cervix
24	chr4:22419200-22476200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr4:22419400-22465800	Weak transcription	HUVEC	blood vessel
26	chr4:22420600-22488000	Weak transcription	Aorta	Aorta
27	chr4:22421200-22442600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr4:22422000-22441400	Weak transcription	Right Ventricle	heart
29	chr4:22422000-22453400	Weak transcription	Esophagus	oesophagus
30	chr4:22422600-22442800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr4:22424400-22457800	Weak transcription	Dnd41	blood
32	chr4:22424600-22448000	Weak transcription	Fetal Kidney	kidney
33	chr4:22426000-22461800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr4:22426200-22442400	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr4:22426200-22443200	Weak transcription	Duodenum Mucosa	Duodenum
36	chr4:22426800-22442800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr4:22427000-22439000	Weak transcription	Primary hematopoietic stem cells	blood
38	chr4:22427400-22444400	Weak transcription	Primary T cells from cord blood	blood
39	chr4:22428600-22460600	Weak transcription	Placenta	Placenta
40	chr4:22429200-22443400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:22429400-22457800	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr4:22429600-22446600	Weak transcription	HSMMtube	muscle
43	chr4:22429800-22438600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr4:22430600-22439400	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr4:22430600-22442800	Weak transcription	Adipose Nuclei	Adipose
46	chr4:22430600-22446200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr4:22430600-22456000	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr4:22430800-22438400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr4:22430800-22442800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr4:22431800-22442800	Weak transcription	Fetal Lung	lung

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