Variant report

Variant	rs7897159
Chromosome Location	chr10:18931580-18931581
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:18927647..18933802-chr10:18937639..18941916,7	K562	blood:
2	chr10:18929497..18932239-chr10:18933812..18935882,2	MCF-7	breast:
3	chr10:18929573..18932544-chr10:18939226..18941814,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241058	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1027193	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs10508562	1.00[CEU][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap]
rs10508563	0.94[CEU][hapmap];0.81[TSI][hapmap]
rs10741111	0.84[JPT][hapmap]
rs10741115	0.85[JPT][hapmap]
rs10764582	0.80[JPT][hapmap]
rs10764601	0.85[JPT][hapmap]
rs10828870	0.80[JPT][hapmap]
rs10828896	0.85[JPT][hapmap]
rs10828975	0.85[JPT][hapmap]
rs10829022	0.85[JPT][hapmap]
rs10829058	0.84[JPT][hapmap]
rs10829070	0.85[JPT][hapmap]
rs11014981	0.94[CHB][hapmap];0.89[JPT][hapmap];0.90[YRI][hapmap]
rs11015312	0.85[JPT][hapmap]
rs11015435	0.82[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[GIH][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11511084	0.94[CHB][hapmap];0.90[JPT][hapmap];0.80[TSI][hapmap];0.90[YRI][hapmap]
rs11540309	0.93[CEU][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs11593617	0.80[EUR][1000 genomes]
rs11597110	0.93[YRI][hapmap]
rs11597737	1.00[EUR][1000 genomes]
rs11812341	0.84[EUR][1000 genomes]
rs11812501	0.95[EUR][1000 genomes]
rs11815228	1.00[CEU][hapmap];0.81[CHB][hapmap];0.80[EUR][1000 genomes]
rs12098599	0.95[EUR][1000 genomes]
rs12762481	0.82[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12762752	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12765026	0.95[EUR][1000 genomes]
rs12765238	0.80[EUR][1000 genomes]
rs12766105	1.00[CEU][hapmap];0.80[JPT][hapmap];0.81[YRI][hapmap];0.80[EUR][1000 genomes]
rs12766314	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs12767046	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12767923	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12768464	0.93[CEU][hapmap]
rs12769425	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12770851	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap];0.80[EUR][1000 genomes]
rs12772009	0.92[CEU][hapmap];0.82[CHB][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12772522	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.90[YRI][hapmap];0.80[EUR][1000 genomes]
rs12774519	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12774593	1.00[CEU][hapmap]
rs12778035	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12779018	0.85[EUR][1000 genomes]
rs12779641	1.00[CEU][hapmap];0.85[TSI][hapmap];0.90[YRI][hapmap]
rs12780652	0.90[AFR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12781208	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12782882	0.95[EUR][1000 genomes]
rs12784387	0.90[JPT][hapmap];0.81[YRI][hapmap]
rs12784555	0.87[CEU][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12784711	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12784986	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12785031	1.00[CEU][hapmap];0.81[YRI][hapmap];0.85[EUR][1000 genomes]
rs1880681	1.00[CEU][hapmap]
rs2130531	0.82[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[GIH][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2171922	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2228645	1.00[CEU][hapmap];0.87[CHB][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap]
rs2272274	0.81[JPT][hapmap]
rs34237250	0.82[EUR][1000 genomes]
rs34359432	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3740104	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3817494	0.85[JPT][hapmap]
rs4237349	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4310518	0.80[CEU][hapmap];0.87[CHB][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.86[LWK][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4314963	1.00[CEU][hapmap];0.81[JPT][hapmap];0.85[TSI][hapmap]
rs4445544	0.83[CHD][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap];0.82[YRI][hapmap]
rs4468242	0.82[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.90[EUR][1000 genomes]
rs4573590	0.84[EUR][1000 genomes]
rs4575162	0.90[EUR][1000 genomes]
rs4628589	0.88[EUR][1000 genomes]
rs4748488	0.85[JPT][hapmap]
rs4748496	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4748497	0.85[EUR][1000 genomes]
rs4748498	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4748499	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55927700	0.84[EUR][1000 genomes]
rs61842187	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6482515	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs6482533	0.85[JPT][hapmap]
rs6482597	0.85[JPT][hapmap]
rs7071300	0.80[EUR][1000 genomes]
rs7072624	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.97[EUR][1000 genomes]
rs7072963	0.82[ASW][hapmap];0.93[CEU][hapmap];0.87[CHB][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.95[EUR][1000 genomes]
rs7074644	0.80[EUR][1000 genomes]
rs7075135	0.80[EUR][1000 genomes]
rs7085318	0.80[EUR][1000 genomes]
rs7086757	0.80[EUR][1000 genomes]
rs7089083	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7093454	0.80[EUR][1000 genomes]
rs7096923	0.87[CEU][hapmap];0.94[CHB][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.96[EUR][1000 genomes]
rs7099260	0.85[JPT][hapmap]
rs7099423	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7100880	0.85[JPT][hapmap]
rs7895784	0.85[JPT][hapmap]
rs7904016	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.80[EUR][1000 genomes]
rs7904949	0.86[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[YRI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7905365	0.93[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs7907891	0.80[EUR][1000 genomes]
rs7909814	0.84[EUR][1000 genomes]
rs7923480	0.80[CEU][hapmap];0.81[JPT][hapmap];0.81[YRI][hapmap];0.85[EUR][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	nsv550042	chr10:18683267-18994583	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer 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	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7897159	STAM	cis	parietal	SCAN
rs7897159	FAM188A	cis	cerebellum	SCAN
rs7897159	ARL5B	Cis_1M	lymphoblastoid	RTeQTL
rs7897159	NSUN6	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18905000-18938200	Weak transcription	Hela-S3	cervix
2	chr10:18916800-18935200	Weak transcription	K562	blood
3	chr10:18916800-18936200	Weak transcription	A549	lung
4	chr10:18916800-18937000	Weak transcription	GM12878-XiMat	blood
5	chr10:18916800-18938400	Weak transcription	HSMMtube	muscle
6	chr10:18916800-18939800	Weak transcription	Aorta	Aorta
7	chr10:18916800-18940200	Weak transcription	Spleen	Spleen
8	chr10:18917000-18932400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr10:18917000-18932600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr10:18917000-18934200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr10:18917000-18934200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr10:18917000-18934400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr10:18917000-18934600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr10:18917000-18934600	Weak transcription	Fetal Brain Female	brain
15	chr10:18917000-18934800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr10:18917000-18934800	Weak transcription	Duodenum Mucosa	Duodenum
17	chr10:18917000-18935000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr10:18917000-18935000	Weak transcription	Primary T cells from cord blood	blood
19	chr10:18917000-18936800	Weak transcription	Brain Germinal Matrix	brain
20	chr10:18917000-18937200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr10:18917000-18937400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr10:18917000-18938000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr10:18917000-18938200	Weak transcription	Primary B cells from peripheral blood	blood
24	chr10:18917000-18938200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr10:18917000-18938200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr10:18917000-18938200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr10:18917000-18938200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr10:18917000-18938200	Weak transcription	Brain Angular Gyrus	brain
29	chr10:18917000-18938400	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr10:18917000-18938400	Weak transcription	Ovary	ovary
31	chr10:18917000-18938400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr10:18917000-18938400	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr10:18917000-18938800	Weak transcription	HSMM	muscle
34	chr10:18917000-18939600	Weak transcription	Placenta	Placenta
35	chr10:18917000-18939800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr10:18917000-18940200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr10:18917000-18940200	Weak transcription	Lung	lung
38	chr10:18917200-18935600	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr10:18917200-18937800	Weak transcription	Adipose Nuclei	Adipose
40	chr10:18921400-18939000	Weak transcription	Right Ventricle	heart
41	chr10:18922600-18939600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr10:18923200-18936600	Weak transcription	Fetal Brain Male	brain
43	chr10:18924800-18937800	Weak transcription	Fetal Lung	lung
44	chr10:18925200-18937600	Weak transcription	Fetal Heart	heart
45	chr10:18925200-18939200	Weak transcription	Stomach Smooth Muscle	stomach
46	chr10:18925600-18939400	Weak transcription	Brain Substantia Nigra	brain
47	chr10:18926000-18940200	Weak transcription	Small Intestine	intestine
48	chr10:18926200-18939200	Weak transcription	Fetal Kidney	kidney
49	chr10:18926400-18938600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr10:18926600-18938200	Weak transcription	NHEK	skin

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