Variant report

Variant	rs1199963
Chromosome Location	chr13:37633525-37633526
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:37573339..37577948-chr13:37631578..37635345,7	K562	blood:
2	chr13:37572711..37577948-chr13:37631792..37635345,6	K562	blood:
3	chr13:37631915..37634175-chr16:87992203..87994742,2	MCF-7	breast:
4	chr13:37573411..37578166-chr13:37631570..37635674,7	MCF-7	breast:
5	chr13:37623154..37627284-chr13:37630471..37633979,5	MCF-7	breast:
6	chr13:37572134..37576910-chr13:37632372..37635841,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172530	Chromatin interaction
ENSG00000120699	Chromatin interaction
ENSG00000120697	Chromatin interaction
ENSG00000102710	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1199951	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1199956	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1199960	0.88[EUR][1000 genomes]
rs1199962	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1199966	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1199972	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1199974	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1199977	0.88[EUR][1000 genomes]
rs1199978	0.88[EUR][1000 genomes]
rs1199979	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1199980	0.88[EUR][1000 genomes]
rs1199981	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1199982	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1199983	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1199984	1.00[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1199986	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1199987	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1199988	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1199989	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12429860	0.82[EUR][1000 genomes]
rs1336755	0.97[EUR][1000 genomes]
rs1543738	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs1764481	0.88[EUR][1000 genomes]
rs1764483	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1764484	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1764486	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1764487	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1764488	0.90[EUR][1000 genomes]
rs1924418	0.95[EUR][1000 genomes]
rs1924419	0.82[AFR][1000 genomes]
rs1924422	0.90[CEU][hapmap];1.00[LWK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs1924426	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1937760	0.90[EUR][1000 genomes]
rs1937761	0.90[CEU][hapmap]
rs2093817	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs2147169	0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes]
rs2181788	0.81[CEU][hapmap]
rs2211618	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2323165	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2323392	0.90[EUR][1000 genomes]
rs2669893	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2769543	0.89[CEU][hapmap]
rs2785620	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2801799	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2997183	1.00[ASW][hapmap]
rs2997189	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2997190	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2997193	0.85[EUR][1000 genomes]
rs3858859	0.94[EUR][1000 genomes]
rs4291799	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes]
rs4941854	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes]
rs4941855	0.87[AMR][1000 genomes]
rs4941856	0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs4943441	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4943442	0.80[EUR][1000 genomes]
rs56158728	0.90[ASN][1000 genomes]
rs6563506	0.81[CEU][hapmap]
rs6563507	0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes]
rs6563508	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6563509	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs675108	0.82[CEU][hapmap]
rs688280	0.83[GIH][hapmap]
rs73175079	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7317750	0.90[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs7320899	0.95[EUR][1000 genomes]
rs7321129	0.90[CEU][hapmap];1.00[LWK][hapmap];0.87[TSI][hapmap];0.82[AFR][1000 genomes]
rs7326688	0.97[EUR][1000 genomes]
rs7334233	0.81[AMR][1000 genomes]
rs7338929	0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs7339296	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7982674	0.81[AMR][1000 genomes]
rs7983986	0.90[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs7989205	0.90[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs7989380	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs7991057	0.90[CEU][hapmap];0.81[AMR][1000 genomes]
rs7995098	0.88[EUR][1000 genomes]
rs7997310	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs8001662	0.95[EUR][1000 genomes]
rs9315459	0.81[AMR][1000 genomes]
rs9531998	0.82[AFR][1000 genomes]
rs9532001	0.90[CEU][hapmap];1.00[LWK][hapmap];0.87[TSI][hapmap];0.82[AFR][1000 genomes]
rs9532004	0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs9532005	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes]
rs9547707	0.90[CEU][hapmap];0.83[GIH][hapmap];0.87[TSI][hapmap]
rs9547715	0.90[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs9547717	0.81[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs9547718	0.90[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs9547721	0.97[EUR][1000 genomes]
rs9547725	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9576153	0.81[AMR][1000 genomes]
rs9576154	0.90[CEU][hapmap];0.81[AMR][1000 genomes]
rs9576162	0.97[EUR][1000 genomes]
rs9603121	0.90[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][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	nsv948975	chr13:37281203-38280430	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv3377840	chr13:37631001-37656330	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1199963	SUPT20H	cis	Whole Blood	GTEx
rs1199963	FAM48A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:37631600-37634600	Active TSS	HSMM	muscle
2	chr13:37631600-37634800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr13:37631800-37634600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr13:37631800-37634600	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr13:37632000-37634600	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr13:37632200-37633600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr13:37632200-37634200	Active TSS	H9 Cell Line	embryonic stem cell
8	chr13:37632200-37634200	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr13:37632200-37634200	Active TSS	NHLF	lung
10	chr13:37632200-37634400	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr13:37632200-37634400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr13:37632200-37634400	Active TSS	Fetal Intestine Small	intestine
13	chr13:37632200-37634400	Active TSS	Stomach Smooth Muscle	stomach
14	chr13:37632200-37634400	Active TSS	A549	lung
15	chr13:37632200-37634600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr13:37632200-37634600	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr13:37632200-37634600	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr13:37632200-37634600	Active TSS	Colonic Mucosa	Colon
19	chr13:37632200-37634800	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr13:37632400-37634000	Active TSS	HMEC	breast
21	chr13:37632400-37634200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr13:37632400-37634200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr13:37632400-37634200	Active TSS	NHDF-Ad	bronchial
24	chr13:37632400-37634400	Active TSS	H1 Cell Line	embryonic stem cell
25	chr13:37632400-37634400	Active TSS	Fetal Brain Male	brain
26	chr13:37632400-37634400	Active TSS	Fetal Intestine Large	intestine
27	chr13:37632400-37634400	Active TSS	Right Atrium	heart
28	chr13:37632400-37634400	Active TSS	Stomach Mucosa	stomach
29	chr13:37632400-37634400	Active TSS	HSMMtube	muscle
30	chr13:37632400-37634400	Active TSS	Osteobl	bone
31	chr13:37632400-37634600	Active TSS	Muscle Satellite Cultured Cells	--
32	chr13:37632400-37634600	Active TSS	K562	blood
33	chr13:37632400-37634800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr13:37632400-37635000	Active TSS	Fetal Kidney	kidney
35	chr13:37632600-37633800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
36	chr13:37632600-37634200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr13:37632600-37634200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr13:37632600-37634200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr13:37632600-37634200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr13:37632600-37634200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr13:37632600-37634200	Active TSS	Fetal Thymus	thymus
42	chr13:37632600-37634400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr13:37632600-37634400	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr13:37632600-37634400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr13:37632600-37634400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr13:37632600-37634400	Active TSS	Fetal Muscle Leg	muscle
47	chr13:37632600-37634600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr13:37632600-37634600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr13:37632600-37634600	Active TSS	Right Ventricle	heart
50	chr13:37632800-37634200	Active TSS	iPS-18 Cell Line	embryonic stem cell

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