Variant report

Variant	rs3740104
Chromosome Location	chr10:18937722-18937723
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:18937279..18942257-chr10:18944156..18951752,16	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152487	Chromatin interaction
ENSG00000165997	Chromatin interaction

Extended variants
information (count: 134 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs1027193	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10508562	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs10508563	0.94[CEU][hapmap];0.81[JPT][hapmap]
rs1055116	0.89[JPT][hapmap]
rs10741091	0.82[JPT][hapmap]
rs10741111	0.95[JPT][hapmap]
rs10741115	0.95[JPT][hapmap]
rs10764582	0.90[JPT][hapmap]
rs10764601	0.95[JPT][hapmap]
rs10764625	0.90[JPT][hapmap]
rs10828851	0.85[JPT][hapmap]
rs10828870	0.90[JPT][hapmap]
rs10828871	0.89[JPT][hapmap]
rs10828896	0.95[JPT][hapmap]
rs10828975	0.95[JPT][hapmap]
rs10829022	0.95[JPT][hapmap]
rs10829037	0.85[JPT][hapmap]
rs10829058	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs10829070	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10829151	0.80[JPT][hapmap]
rs11014981	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[ASN][1000 genomes]
rs11015312	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs11015435	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11511084	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[ASN][1000 genomes]
rs11540309	0.93[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11593617	0.83[AMR][1000 genomes]
rs11597110	0.94[YRI][hapmap]
rs11597737	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11812341	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11812501	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11815228	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[AMR][1000 genomes]
rs12098599	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12219183	0.81[ASN][1000 genomes]
rs12359758	0.82[ASN][1000 genomes]
rs12762481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12762752	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12764334	0.84[AMR][1000 genomes]
rs12764398	0.81[AMR][1000 genomes]
rs12765026	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12765238	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12766105	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes]
rs12766314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12767046	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12767923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12768464	0.93[CEU][hapmap]
rs12769425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12770851	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12772009	0.93[CEU][hapmap];0.88[CHB][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12772522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12774519	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12774593	0.83[CEU][hapmap];0.83[CHB][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes]
rs12775419	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12778035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12778992	0.81[AMR][1000 genomes]
rs12779018	0.83[EUR][1000 genomes]
rs12779641	1.00[CEU][hapmap];0.90[YRI][hapmap]
rs12779694	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12780652	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12781208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12782882	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12784387	0.83[CHB][hapmap]
rs12784555	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs12784711	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12784986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12785031	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1880681	1.00[CEU][hapmap]
rs2130531	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2171922	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.86[YRI][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2228645	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes]
rs2272274	0.90[JPT][hapmap]
rs34237250	0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34359432	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35766272	0.81[ASN][1000 genomes]
rs3740102	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs3817494	0.95[JPT][hapmap]
rs4237349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4310518	0.80[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4314963	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs4445544	0.83[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap]
rs4468242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4573590	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4575162	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4628589	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4747355	0.87[AMR][1000 genomes]
rs4748481	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs4748487	0.87[AMR][1000 genomes]
rs4748488	0.95[JPT][hapmap]
rs4748490	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4748496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4748497	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4748498	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4748499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5022622	0.84[JPT][hapmap]
rs55927700	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57066269	0.81[ASN][1000 genomes]
rs61663155	0.90[AMR][1000 genomes]
rs61842187	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6482515	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs6482533	0.95[JPT][hapmap]
rs6482597	0.95[JPT][hapmap]
rs7071300	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7072624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7072963	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7074644	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7075135	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7081461	0.89[JPT][hapmap]
rs7081977	0.82[ASN][1000 genomes]
rs7085318	0.83[AMR][1000 genomes]
rs7086757	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7088091	0.85[JPT][hapmap]
rs7089083	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7093454	0.83[AMR][1000 genomes]
rs7096923	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7099260	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7099423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7100880	0.95[JPT][hapmap]
rs7895784	0.95[JPT][hapmap]
rs7897159	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]
rs7898513	0.81[JPT][hapmap]
rs7898781	0.81[ASN][1000 genomes]
rs7899017	0.81[ASN][1000 genomes]
rs7904016	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7904949	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7905365	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7907891	0.83[AMR][1000 genomes]
rs7909814	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7917584	0.81[JPT][hapmap]
rs7919487	0.84[AMR][1000 genomes]
rs7922550	0.86[JPT][hapmap]
rs7922829	0.86[JPT][hapmap]
rs7923480	0.80[CEU][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.83[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	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
2	nsv466762	chr10:18932172-18976659	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv550121	chr10:18932172-18976659	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3740104	ARL5B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18905000-18938200	Weak transcription	Hela-S3	cervix
2	chr10:18916800-18938400	Weak transcription	HSMMtube	muscle
3	chr10:18916800-18939800	Weak transcription	Aorta	Aorta
4	chr10:18916800-18940200	Weak transcription	Spleen	Spleen
5	chr10:18917000-18938000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr10:18917000-18938200	Weak transcription	Primary B cells from peripheral blood	blood
7	chr10:18917000-18938200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr10:18917000-18938200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr10:18917000-18938200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr10:18917000-18938200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr10:18917000-18938200	Weak transcription	Brain Angular Gyrus	brain
12	chr10:18917000-18938400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr10:18917000-18938400	Weak transcription	Ovary	ovary
14	chr10:18917000-18938400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr10:18917000-18938400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr10:18917000-18938800	Weak transcription	HSMM	muscle
17	chr10:18917000-18939600	Weak transcription	Placenta	Placenta
18	chr10:18917000-18939800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr10:18917000-18940200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr10:18917000-18940200	Weak transcription	Lung	lung
21	chr10:18917200-18937800	Weak transcription	Adipose Nuclei	Adipose
22	chr10:18921400-18939000	Weak transcription	Right Ventricle	heart
23	chr10:18922600-18939600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr10:18924800-18937800	Weak transcription	Fetal Lung	lung
25	chr10:18925200-18939200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr10:18925600-18939400	Weak transcription	Brain Substantia Nigra	brain
27	chr10:18926000-18940200	Weak transcription	Small Intestine	intestine
28	chr10:18926200-18939200	Weak transcription	Fetal Kidney	kidney
29	chr10:18926400-18938600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr10:18926600-18938200	Weak transcription	NHEK	skin
31	chr10:18927400-18939600	Weak transcription	Pancreas	Pancrea
32	chr10:18927800-18937800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr10:18928000-18938400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr10:18928200-18938200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr10:18928200-18939400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr10:18928400-18938800	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr10:18928800-18937800	Weak transcription	Brain Anterior Caudate	brain
38	chr10:18928800-18939600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr10:18928800-18939600	Weak transcription	Gastric	stomach
40	chr10:18929000-18939000	Weak transcription	Rectal Smooth Muscle	rectum
41	chr10:18929600-18938800	Weak transcription	Fetal Intestine Large	intestine
42	chr10:18930800-18937800	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr10:18931000-18939600	Weak transcription	Fetal Muscle Leg	muscle
44	chr10:18931400-18938000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr10:18931600-18937800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr10:18932000-18938200	Weak transcription	Colon Smooth Muscle	Colon
47	chr10:18932600-18937800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr10:18932800-18938400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr10:18933200-18937800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr10:18933200-18939400	Weak transcription	Thymus	Thymus

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