Variant report

Variant	rs7078711
Chromosome Location	chr10:5744985-5744986
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:5732181..5739053-chr10:5741617..5746199,6	MCF-7	breast:
2	chr10:5487728..5489402-chr10:5743832..5746682,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173848	Chromatin interaction
ENSG00000108021	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10737012	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10737013	0.91[EUR][1000 genomes]
rs10737019	0.88[EUR][1000 genomes]
rs10752069	0.88[EUR][1000 genomes]
rs10752110	0.82[EUR][1000 genomes]
rs10795347	0.84[EUR][1000 genomes]
rs10795485	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10795488	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10795510	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10795515	0.87[EUR][1000 genomes]
rs10795520	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs10795541	0.88[CEU][hapmap];0.93[TSI][hapmap]
rs10905065	0.96[CEU][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs10905137	0.83[EUR][1000 genomes]
rs11254266	0.81[CEU][hapmap];0.82[CHB][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.86[TSI][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11255228	0.81[EUR][1000 genomes]
rs11598374	0.82[ASN][1000 genomes]
rs12571639	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1317420	0.89[EUR][1000 genomes]
rs1567706	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1567707	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1858447	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2175630	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2244755	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2380199	0.92[CEU][hapmap]
rs2380202	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2380203	0.80[CEU][hapmap]
rs2497	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2797488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2890365	0.88[CEU][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes]
rs2892078	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3736462	0.83[EUR][1000 genomes]
rs4237365	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4748307	0.81[EUR][1000 genomes]
rs4748913	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4748916	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60840965	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61832743	0.81[EUR][1000 genomes]
rs6602240	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6602278	0.86[TSI][hapmap]
rs7071811	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7089100	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7096742	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7100576	0.89[EUR][1000 genomes]
rs7896749	0.88[EUR][1000 genomes]
rs7906719	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7909988	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7913067	0.96[CEU][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs9423726	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9423930	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9423948	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534685	chr10:4914018-5853324	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer 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 miRNA target site	68 gene(s)	inside rSNPs	diseases
2	esv2759729	chr10:5557024-5804780	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	esv2758209	chr10:5637111-5804780	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	esv1796213	chr10:5716555-5766165	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv522415	chr10:5721653-5768493	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv34147	chr10:5726821-6105717	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats 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	42 gene(s)	inside rSNPs	diseases
7	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv1050663	chr10:5737979-5785918	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv528504	chr10:5739054-5754611	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7078711	CALML5	cis	parietal	SCAN
rs7078711	GDI2	cis	cerebellum	SCAN
rs7078711	GDI2	Cis_1M	lymphoblastoid	RTeQTL
rs7078711	GDI2	cis	parietal	SCAN
rs7078711	GDI2	cis	uninvolved skin	skin_eQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5728800-5746800	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr10:5734800-5763400	Weak transcription	HSMM	muscle
3	chr10:5735200-5749000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr10:5735200-5750600	Weak transcription	Gastric	stomach
5	chr10:5735200-5767000	Weak transcription	Fetal Muscle Leg	muscle
6	chr10:5735400-5750800	Weak transcription	Spleen	Spleen
7	chr10:5735400-5761600	Weak transcription	NHEK	skin
8	chr10:5735400-5762000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr10:5735800-5752800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr10:5736200-5751600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr10:5736400-5753000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr10:5738200-5745200	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr10:5738600-5752400	Weak transcription	Primary B cells from cord blood	blood
14	chr10:5738600-5752800	Weak transcription	Right Atrium	heart
15	chr10:5738600-5769000	Weak transcription	Left Ventricle	heart
16	chr10:5739400-5745000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr10:5739600-5752800	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr10:5740200-5752000	Weak transcription	Stomach Mucosa	stomach
19	chr10:5740200-5752800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr10:5740400-5768600	Weak transcription	Psoas Muscle	Psoas
21	chr10:5741400-5749000	Weak transcription	K562	blood
22	chr10:5741400-5760600	Weak transcription	Small Intestine	intestine
23	chr10:5741400-5765600	Weak transcription	A549	lung
24	chr10:5741600-5747200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr10:5741600-5750200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr10:5741600-5753400	Weak transcription	Primary B cells from peripheral blood	blood
27	chr10:5742200-5748800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr10:5742600-5749000	Weak transcription	Primary T cells from cord blood	blood
29	chr10:5743200-5746800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr10:5743200-5752400	Weak transcription	Brain Substantia Nigra	brain
31	chr10:5743200-5753600	Weak transcription	HepG2	liver
32	chr10:5743200-5762600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr10:5743600-5749000	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr10:5744200-5746800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr10:5744200-5748200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr10:5744200-5749400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr10:5744200-5753000	Weak transcription	Primary hematopoietic stem cells	blood
38	chr10:5744400-5745000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr10:5744800-5745000	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr10:5744800-5745000	Enhancers	Liver	Liver
41	chr10:5744800-5745200	Enhancers	Breast Myoepithelial Primary Cells	Breast

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