Variant report

Variant	rs1536338
Chromosome Location	chr10:838378-838379
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	chr10:180500..182203-chr10:836766..839418,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000015171	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1000278	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1057303	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1057304	0.88[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10752020	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10752021	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs10904571	0.85[ASN][1000 genomes]
rs10904572	0.82[ASN][1000 genomes]
rs10904575	0.86[CHB][hapmap]
rs11253448	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11253449	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11253451	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11253471	0.86[CHB][hapmap]
rs12243303	0.92[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12413052	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12413228	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12413763	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12573825	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1555895	0.80[CEU][hapmap]
rs1555896	0.82[ASN][1000 genomes]
rs1555897	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1555898	0.84[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2148368	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2274375	0.88[ASN][1000 genomes]
rs2274376	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2892159	0.88[CEU][hapmap];0.84[ASN][1000 genomes]
rs35913002	0.86[ASN][1000 genomes]
rs3763722	0.89[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs4097329	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4229	0.92[CEU][hapmap];0.90[CHB][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4362075	0.89[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.82[EUR][1000 genomes]
rs4880743	0.95[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs4881529	0.88[CHD][hapmap];0.85[JPT][hapmap]
rs4881530	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs4881532	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4881535	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4881537	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4881538	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61831437	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61831439	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7071801	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7077992	0.81[CHB][hapmap]
rs7080989	0.92[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7091806	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7095043	0.84[JPT][hapmap]
rs748112	0.89[CEU][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs749297	0.92[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs750370	0.81[JPT][hapmap]
rs752375	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7703	0.92[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7899871	0.85[CHB][hapmap]
rs7913077	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7919815	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9124	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs997615	0.92[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916591	chr10:224406-1088734	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv540386	chr10:224406-1197416	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1050252	chr10:375035-839594	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv540397	chr10:375035-839594	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv1048859	chr10:442805-887622	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
6	nsv1039958	chr10:450753-889167	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
7	nsv540400	chr10:450753-889167	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
8	nsv549753	chr10:458477-894838	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
9	nsv1044857	chr10:577396-856059	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
10	nsv540402	chr10:577396-856059	Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
11	nsv528733	chr10:577444-838378	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
12	nsv1036675	chr10:600206-839594	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
13	nsv1054659	chr10:611444-1133578	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
14	nsv948602	chr10:708293-944641	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv949063	chr10:708293-974870	Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
16	nsv466697	chr10:734229-1129527	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
17	nsv549765	chr10:734229-1129527	Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
18	nsv1036316	chr10:748848-849979	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
19	nsv894718	chr10:763714-861390	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
20	nsv1045119	chr10:766867-855251	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
21	nsv1043812	chr10:776547-981126	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
22	nsv540406	chr10:776547-981126	Bivalent Enhancer Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
23	nsv530116	chr10:776548-1401075	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
24	nsv948978	chr10:813426-1019115	Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
25	nsv1048707	chr10:834439-915534	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
26	esv3356062	chr10:835552-839750	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
27	nsv466698	chr10:836115-888073	ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
28	nsv549766	chr10:836115-888073	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1536338	DIP2C	cis	cerebellum	SCAN
rs1536338	LARP5	Cis_1M	lymphoblastoid	RTeQTL
rs1536338	GTPBP4	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:831400-850000	Weak transcription	Fetal Heart	heart
2	chr10:835000-841800	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr10:835400-838800	Weak transcription	NHDF-Ad	bronchial
4	chr10:835400-843000	Weak transcription	Aorta	Aorta
5	chr10:835600-838800	Weak transcription	NH-A	brain
6	chr10:835600-841400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr10:835600-841800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr10:835600-842800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr10:835600-853000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr10:835800-838800	Weak transcription	NHLF	lung
11	chr10:835800-839600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr10:835800-852800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr10:836000-839200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr10:836000-840200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr10:836000-841400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr10:836000-842000	Weak transcription	A549	lung
17	chr10:836000-849000	Weak transcription	Right Ventricle	heart
18	chr10:836000-849400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr10:836000-852000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr10:836000-852800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr10:836200-840600	Weak transcription	Spleen	Spleen
22	chr10:836200-842800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr10:836200-850200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr10:836200-852000	Weak transcription	Ovary	ovary
25	chr10:836200-852400	Weak transcription	Brain Hippocampus Middle	brain
26	chr10:836200-852600	Weak transcription	Osteobl	bone
27	chr10:836400-839000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr10:836400-848600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr10:836400-850400	Weak transcription	Duodenum Mucosa	Duodenum
30	chr10:836600-853000	Weak transcription	Stomach Mucosa	stomach
31	chr10:837000-842800	Weak transcription	Placenta	Placenta
32	chr10:837200-843000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr10:837800-838400	Weak transcription	Lung	lung
34	chr10:837800-848400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr10:838000-838400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr10:838000-838600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr10:838000-838600	Weak transcription	Fetal Muscle Leg	muscle
38	chr10:838000-838800	Enhancers	HSMMtube	muscle
39	chr10:838000-839400	Enhancers	Fetal Stomach	stomach
40	chr10:838000-843000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr10:838000-851200	Weak transcription	Gastric	stomach
42	chr10:838200-838400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr10:838200-839200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr10:838200-839400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr10:838200-839400	Enhancers	Muscle Satellite Cultured Cells	--
46	chr10:838200-839400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr10:838200-839400	Enhancers	HSMM	muscle
48	chr10:838200-840000	Weak transcription	Esophagus	oesophagus

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