Variant report

Variant	rs2636968
Chromosome Location	chr5:118838068-118838069
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	chr5:118831350..118835449-chr5:118835713..118839843,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133835	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs2257900	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2257901	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2455463	0.87[ASN][1000 genomes]
rs2459726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs246965	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs246966	0.81[MKK][hapmap]
rs246967	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2546210	0.92[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs257970	1.00[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs257976	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs257978	0.90[ASN][1000 genomes]
rs26181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs26184	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2636961	0.81[ASW][hapmap];0.96[CEU][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2636962	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2636964	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2678070	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap];0.94[ASN][1000 genomes]
rs2678074	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2678076	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2678091	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs27938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs32640	0.84[ASN][1000 genomes]
rs32651	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs32662	0.83[TSI][hapmap]
rs32664	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32665	0.81[TSI][hapmap]
rs382719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3850202	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs389760	0.82[ASN][1000 genomes]
rs39970	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs422297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs426899	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs439954	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs442923	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs450118	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs460274	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs461108	0.91[MEX][hapmap]
rs463098	1.00[CEU][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs463513	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs467076	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6875595	0.91[MEX][hapmap]
rs7721602	0.91[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427732	chr5:118730999-119034741	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1024455	chr5:118770429-119487982	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1016271	chr5:118836891-119487982	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv2486573	chr5:118837315-118838827	Weak transcription Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2636968	HSD17B4	Cis_1M	lymphoblastoid	RTeQTL
rs2636968	SNX24	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118791800-118846600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:118794800-118861200	Weak transcription	HSMM	muscle
3	chr5:118804200-118879600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr5:118805200-118839400	Weak transcription	NHEK	skin
5	chr5:118806000-118846400	Weak transcription	Esophagus	oesophagus
6	chr5:118806000-118846400	Weak transcription	Spleen	Spleen
7	chr5:118806200-118844800	Weak transcription	Thymus	Thymus
8	chr5:118806200-118846400	Weak transcription	Pancreas	Pancrea
9	chr5:118806200-118855600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr5:118806400-118845000	Weak transcription	Fetal Stomach	stomach
11	chr5:118806400-118846400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr5:118806800-118845400	Weak transcription	Fetal Heart	heart
13	chr5:118808000-118839600	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr5:118808000-118839800	Weak transcription	Psoas Muscle	Psoas
15	chr5:118811200-118839600	Weak transcription	Brain Germinal Matrix	brain
16	chr5:118812000-118846400	Weak transcription	NHLF	lung
17	chr5:118814000-118838200	Weak transcription	Fetal Intestine Small	intestine
18	chr5:118814000-118845000	Weak transcription	Gastric	stomach
19	chr5:118814000-118845200	Weak transcription	Aorta	Aorta
20	chr5:118814800-118839400	Weak transcription	Right Ventricle	heart
21	chr5:118814800-118844800	Weak transcription	Lung	lung
22	chr5:118815400-118839000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr5:118815800-118839000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr5:118815800-118845400	Weak transcription	HMEC	breast
25	chr5:118816000-118844000	Weak transcription	Hela-S3	cervix
26	chr5:118816000-118847000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr5:118816800-118839600	Strong transcription	Adipose Nuclei	Adipose
28	chr5:118817000-118846400	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr5:118817200-118839600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr5:118818400-118839600	Weak transcription	Fetal Kidney	kidney
31	chr5:118819000-118839200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr5:118819600-118844400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr5:118820000-118839000	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr5:118820000-118839600	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr5:118820200-118838600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr5:118820200-118846400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr5:118820400-118838800	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr5:118821000-118839600	Strong transcription	Liver	Liver
39	chr5:118821000-118843800	Weak transcription	NHDF-Ad	bronchial
40	chr5:118824200-118838400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr5:118827600-118847800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr5:118828000-118840400	Weak transcription	Osteobl	bone
43	chr5:118829200-118840200	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr5:118829600-118839600	Strong transcription	Duodenum Mucosa	Duodenum
45	chr5:118829800-118844800	Weak transcription	Rectal Smooth Muscle	rectum
46	chr5:118830400-118845200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr5:118831000-118840200	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr5:118832400-118839600	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr5:118832400-118878200	Weak transcription	NH-A	brain
50	chr5:118832600-118844400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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