Variant report

Variant	rs673964
Chromosome Location	chr10:6488790-6488791
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:6486742..6489552-chr10:6709675..6712349,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10906569	0.86[EUR][1000 genomes]
rs11258536	0.84[TSI][hapmap]
rs11258759	0.81[EUR][1000 genomes]
rs11258762	0.83[EUR][1000 genomes]
rs11258959	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11258960	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11814744	0.93[YRI][hapmap]
rs11816284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs11817284	0.92[YRI][hapmap]
rs12146312	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2453	0.86[CHD][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs4364968	1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[MEX][hapmap];0.95[ASN][1000 genomes]
rs4750434	0.81[EUR][1000 genomes]
rs4750439	0.86[CHD][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs4750457	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4750461	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4750470	1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs4750491	0.90[MEX][hapmap]
rs4750495	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs586457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs593608	1.00[YRI][hapmap]
rs594841	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs630196	1.00[YRI][hapmap]
rs6602699	0.92[ASN][1000 genomes]
rs670804	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs677986	0.83[CEU][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs681803	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs688391	0.81[MEX][hapmap]
rs688853	1.00[YRI][hapmap]
rs7076533	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7099451	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7918373	1.00[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs7920048	0.83[EUR][1000 genomes]
rs943456	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs944712	0.83[EUR][1000 genomes]
rs944713	0.83[EUR][1000 genomes]
rs944715	0.83[CEU][hapmap];0.86[CHD][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1053440	chr10:6354798-6669469	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs673964	PLCD3	trans	parietal	SCAN
rs673964	CALML5	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6456200-6496600	Weak transcription	Pancreas	Pancrea
2	chr10:6464600-6490600	Strong transcription	Primary T cells from cord blood	blood
3	chr10:6465800-6496200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr10:6465800-6496600	Weak transcription	Psoas Muscle	Psoas
5	chr10:6465800-6501400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr10:6467400-6496200	Weak transcription	Lung	lung
7	chr10:6468200-6496800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr10:6471200-6490200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr10:6474200-6490400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr10:6477400-6503600	Weak transcription	Gastric	stomach
11	chr10:6478800-6491000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr10:6480200-6501000	Weak transcription	Ovary	ovary
13	chr10:6480800-6497600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr10:6481200-6500200	Weak transcription	Fetal Intestine Small	intestine
15	chr10:6481400-6497800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr10:6484000-6489400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr10:6484000-6489400	Weak transcription	Fetal Muscle Leg	muscle
18	chr10:6484000-6496200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr10:6484200-6496200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr10:6484200-6496400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr10:6484600-6489400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr10:6484600-6496600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr10:6486600-6488800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr10:6487200-6489000	Genic enhancers	Primary T cells fromperipheralblood	blood
25	chr10:6487200-6490600	Genic enhancers	Fetal Thymus	thymus
26	chr10:6488200-6488800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr10:6488200-6488800	Weak transcription	Dnd41	blood
28	chr10:6488200-6489400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr10:6488200-6489400	Strong transcription	Skeletal Muscle Male	skeletal muscle
30	chr10:6488200-6489600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr10:6488200-6489600	Weak transcription	Brain Angular Gyrus	brain
32	chr10:6488200-6496200	Weak transcription	Primary hematopoietic stem cells	blood
33	chr10:6488200-6496200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr10:6488200-6496200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr10:6488200-6496200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr10:6488200-6496200	Weak transcription	Brain Substantia Nigra	brain
37	chr10:6488200-6496400	Weak transcription	Adipose Nuclei	Adipose
38	chr10:6488200-6496400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr10:6488200-6497600	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr10:6488200-6499600	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr10:6488200-6500200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr10:6488200-6502000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr10:6488400-6488800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr10:6488400-6489200	Weak transcription	Fetal Stomach	stomach
45	chr10:6488400-6489400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr10:6488400-6489400	Weak transcription	Brain Cingulate Gyrus	brain
47	chr10:6488400-6489600	Weak transcription	Brain Hippocampus Middle	brain
48	chr10:6488400-6490600	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr10:6488400-6490800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr10:6488400-6496600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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