Variant report

Variant	rs10934674
Chromosome Location	chr3:93812793-93812794
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:93781320..93783928-chr3:93812018..93813726,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178694	Chromatin interaction
ENSG00000178700	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10433405	0.88[CEU][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56260303	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56364604	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61739170	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62265480	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62265486	0.88[EUR][1000 genomes]
rs62265488	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62266146	0.83[EUR][1000 genomes]
rs62266147	0.83[EUR][1000 genomes]
rs62266150	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62266151	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62266152	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6771536	1.00[YRI][hapmap]
rs7432837	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7627752	1.00[YRI][hapmap]
rs8178591	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs8178607	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869241	chr3:93527675-94504491	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv998173	chr3:93575084-94427403	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv536644	chr3:93575084-94427403	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1008711	chr3:93575284-94427264	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv536646	chr3:93575284-94427264	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv491829	chr3:93575285-94427263	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	esv1795060	chr3:93602038-93848525	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	n/a
8	esv1791740	chr3:93602927-93849247	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	n/a
9	esv2755326	chr3:93605126-93882750	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	n/a
10	nsv1013107	chr3:93654100-94102212	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	nsv536648	chr3:93654100-94102212	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv1004176	chr3:93654100-94502551	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
13	nsv877162	chr3:93779664-94278078	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv877163	chr3:93795972-94047775	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10934674	DHFRL1	cis	cerebellum	SCAN
rs10934674	EPHA3	trans	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:93782800-93813400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:93782800-93848200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:93782800-93849400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr3:93783000-93813800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr3:93783000-93813800	Weak transcription	Right Ventricle	heart
6	chr3:93783200-93824600	Weak transcription	NHEK	skin
7	chr3:93783200-93851600	Weak transcription	HMEC	breast
8	chr3:93783400-93813800	Weak transcription	Colon Smooth Muscle	Colon
9	chr3:93783400-93833000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:93783600-93837800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:93784600-93814000	Weak transcription	A549	lung
12	chr3:93784600-93817400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr3:93784800-93820200	Weak transcription	Hela-S3	cervix
14	chr3:93785600-93834400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr3:93786200-93834600	Weak transcription	Brain Substantia Nigra	brain
16	chr3:93786400-93830800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:93786800-93816400	Weak transcription	HUVEC	blood vessel
18	chr3:93786800-93849800	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr3:93788200-93817000	Weak transcription	NHDF-Ad	bronchial
20	chr3:93791400-93813800	Weak transcription	Brain Hippocampus Middle	brain
21	chr3:93791400-93814000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:93791400-93841200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr3:93792000-93816600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:93792200-93833200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:93795400-93817200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr3:93795600-93817200	Weak transcription	NH-A	brain
27	chr3:93795600-93822000	Weak transcription	HSMMtube	muscle
28	chr3:93795600-93847000	Weak transcription	Osteobl	bone
29	chr3:93796000-93814000	Weak transcription	Brain Germinal Matrix	brain
30	chr3:93796000-93814000	Weak transcription	Esophagus	oesophagus
31	chr3:93796000-93857800	Weak transcription	Fetal Brain Male	brain
32	chr3:93799000-93851600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr3:93799800-93813000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr3:93799800-93813200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr3:93800000-93813800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr3:93800000-93817200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr3:93800000-93830800	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr3:93800200-93814000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr3:93800200-93814200	Weak transcription	Colonic Mucosa	Colon
40	chr3:93800200-93851000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:93802200-93816600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr3:93802200-93830800	Weak transcription	Fetal Kidney	kidney
43	chr3:93802400-93814000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr3:93802400-93817400	Weak transcription	Brain Angular Gyrus	brain
45	chr3:93802400-93849600	Weak transcription	Stomach Mucosa	stomach
46	chr3:93802600-93817400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr3:93802600-93851800	Weak transcription	Small Intestine	intestine
48	chr3:93802800-93813200	Weak transcription	HepG2	liver
49	chr3:93802800-93817000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr3:93802800-93830800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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