Variant report

Variant	rs12640894
Chromosome Location	chr4:88357015-88357016
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:88342347..88345109-chr4:88355579..88358193,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170502	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10000196	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10009948	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10023606	0.97[ASN][1000 genomes]
rs10024781	0.94[ASN][1000 genomes]
rs10030035	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10032122	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10084883	0.97[ASN][1000 genomes]
rs12640451	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12648665	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12650763	0.97[ASN][1000 genomes]
rs12651034	0.97[ASN][1000 genomes]
rs28366407	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28415220	0.92[ASN][1000 genomes]
rs28437709	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28493315	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28493566	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28529046	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28535549	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28696943	0.90[ASN][1000 genomes]
rs28712618	0.97[ASN][1000 genomes]
rs28718986	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28762371	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28805573	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34027531	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4411944	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55824708	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56153912	0.99[ASN][1000 genomes]
rs58192677	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67121411	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs68045074	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72652067	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7665115	0.97[ASN][1000 genomes]
rs7673763	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7677249	0.97[ASN][1000 genomes]
rs7680878	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7690728	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9995987	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9998212	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[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	nsv1002789	chr4:88239340-88606485	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12640894	HSD17B11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88344400-88398600	Weak transcription	Gastric	stomach
2	chr4:88345200-88362800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr4:88345200-88363000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr4:88345200-88400000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr4:88345200-88416400	Weak transcription	Colonic Mucosa	Colon
6	chr4:88345400-88357200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr4:88345400-88357600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr4:88345400-88359400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr4:88345400-88359400	Weak transcription	Fetal Thymus	thymus
10	chr4:88345400-88361400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr4:88345400-88363400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr4:88345400-88372400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr4:88345400-88378800	Weak transcription	A549	lung
14	chr4:88345800-88357200	Weak transcription	Left Ventricle	heart
15	chr4:88345800-88357400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr4:88345800-88360800	Weak transcription	Brain Anterior Caudate	brain
17	chr4:88345800-88363400	Weak transcription	Right Ventricle	heart
18	chr4:88345800-88372200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr4:88346000-88359400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:88346000-88359400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr4:88346000-88363200	Weak transcription	Primary B cells from cord blood	blood
22	chr4:88346000-88364200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr4:88346200-88359200	Weak transcription	NHDF-Ad	bronchial
24	chr4:88346200-88361000	Weak transcription	Colon Smooth Muscle	Colon
25	chr4:88346200-88363200	Weak transcription	K562	blood
26	chr4:88346200-88370600	Weak transcription	Thymus	Thymus
27	chr4:88346200-88382600	Weak transcription	NHLF	lung
28	chr4:88346400-88357200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr4:88346400-88357200	Weak transcription	Brain Angular Gyrus	brain
30	chr4:88346400-88357200	Weak transcription	Fetal Brain Female	brain
31	chr4:88346400-88357200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr4:88346400-88357200	Weak transcription	GM12878-XiMat	blood
33	chr4:88346400-88357200	Weak transcription	HUVEC	blood vessel
34	chr4:88346400-88357400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr4:88346400-88362600	Weak transcription	Brain Substantia Nigra	brain
36	chr4:88346400-88366200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr4:88346400-88369600	Weak transcription	Right Atrium	heart
38	chr4:88346400-88372200	Weak transcription	Aorta	Aorta
39	chr4:88346400-88379400	Weak transcription	Small Intestine	intestine
40	chr4:88346600-88360000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr4:88346600-88360200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr4:88346600-88362800	Weak transcription	Osteobl	bone
43	chr4:88346600-88363800	Weak transcription	HMEC	breast
44	chr4:88346600-88371600	Weak transcription	Spleen	Spleen
45	chr4:88346600-88372200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr4:88346600-88410400	Weak transcription	Esophagus	oesophagus
47	chr4:88346800-88371400	Weak transcription	Lung	lung
48	chr4:88347200-88360000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr4:88347200-88361400	Weak transcription	Ovary	ovary
50	chr4:88347200-88366000	Weak transcription	NH-A	brain

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