Variant report

Variant	rs10948125
Chromosome Location	chr6:44107798-44107799
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:44101660..44104148-chr6:44106994..44109571,3	MCF-7	breast:
2	chr6:44106717..44108316-chr6:44214110..44216405,3	K562	blood:
3	chr6:44103703..44105996-chr6:44106065..44109436,3	MCF-7	breast:
4	chr6:44107297..44110338-chr6:44222390..44225778,3	K562	blood:
5	chr6:44101577..44103606-chr6:44104926..44108402,3	MCF-7	breast:
6	chr6:44107494..44110338-chr6:44222390..44224695,3	K562	blood:

Variant related genes	Relation type
ENSG00000096384	Chromatin interaction
ENSG00000157593	Chromatin interaction
ENSG00000137216	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10428726	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10456527	0.87[CEU][hapmap]
rs10755724	0.80[EUR][1000 genomes]
rs10807295	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10948122	1.00[CHB][hapmap];0.96[ASN][1000 genomes]
rs10948123	0.96[ASN][1000 genomes]
rs10948126	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11966587	0.96[ASN][1000 genomes]
rs11967633	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11968386	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12525049	0.89[ASN][1000 genomes]
rs12526662	0.96[ASN][1000 genomes]
rs12664793	0.96[ASN][1000 genomes]
rs2096200	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3188	1.00[JPT][hapmap]
rs35738079	0.93[ASN][1000 genomes]
rs41282654	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4711765	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4714744	0.96[ASN][1000 genomes]
rs4714749	0.96[ASN][1000 genomes]
rs4714753	0.84[AFR][1000 genomes]
rs55862642	0.96[ASN][1000 genomes]
rs59028814	0.96[ASN][1000 genomes]
rs60245793	0.96[ASN][1000 genomes]
rs60691447	0.96[ASN][1000 genomes]
rs6912142	0.93[ASN][1000 genomes]
rs700006	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs713050	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs73733834	0.93[ASN][1000 genomes]
rs7738970	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7756198	0.84[AFR][1000 genomes]
rs7771710	0.96[ASN][1000 genomes]
rs9349273	0.84[AFR][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	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS 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	201 gene(s)	inside rSNPs	diseases
2	nsv462935	chr6:44046143-44117607	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv603002	chr6:44046143-44117607	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10948125	FRS3	cis	cerebellum	SCAN
rs10948125	CIB1	trans	lymphoblastoid	seeQTL
rs10948125	GPR110	cis	cerebellum	SCAN
rs10948125	SLC25A27	cis	cerebellum	SCAN
rs10948125	MRPL2	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44096600-44119400	Weak transcription	Right Atrium	heart
2	chr6:44096800-44119400	Weak transcription	HUVEC	blood vessel
3	chr6:44098000-44114800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr6:44098000-44119400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr6:44098000-44119400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr6:44100400-44119000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr6:44101200-44119400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr6:44101400-44119400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:44101600-44108600	Weak transcription	NH-A	brain
10	chr6:44101600-44113600	Weak transcription	Hela-S3	cervix
11	chr6:44101600-44118400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:44101800-44112400	Strong transcription	Fetal Brain Female	brain
13	chr6:44101800-44112600	Strong transcription	Brain Germinal Matrix	brain
14	chr6:44101800-44119200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:44101800-44124000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr6:44102000-44109600	Strong transcription	HepG2	liver
17	chr6:44102000-44113400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr6:44102000-44115200	Weak transcription	Small Intestine	intestine
19	chr6:44102000-44117600	Weak transcription	Fetal Heart	heart
20	chr6:44102000-44118600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr6:44102000-44119400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:44102200-44109200	Strong transcription	Thymus	Thymus
23	chr6:44102200-44109600	Strong transcription	Adipose Nuclei	Adipose
24	chr6:44102200-44112200	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr6:44102200-44112200	Strong transcription	Skeletal Muscle Male	skeletal muscle
26	chr6:44102200-44112400	Strong transcription	Skeletal Muscle Female	skeletal muscle
27	chr6:44102200-44112400	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr6:44102200-44112400	Strong transcription	NHEK	skin
29	chr6:44102200-44117800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr6:44102200-44118000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:44102200-44118400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr6:44102200-44119800	Strong transcription	Fetal Intestine Small	intestine
33	chr6:44102400-44108800	Strong transcription	Rectal Smooth Muscle	rectum
34	chr6:44102400-44109600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr6:44102400-44109600	Strong transcription	Liver	Liver
36	chr6:44102400-44110800	Strong transcription	Esophagus	oesophagus
37	chr6:44102400-44112000	Strong transcription	Lung	lung
38	chr6:44102400-44112400	Strong transcription	Placenta	Placenta
39	chr6:44102400-44112600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr6:44102400-44113400	Weak transcription	Fetal Brain Male	brain
41	chr6:44102400-44118000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr6:44102400-44118000	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr6:44102400-44118200	Strong transcription	Duodenum Mucosa	Duodenum
44	chr6:44102400-44118200	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr6:44102400-44119400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:44102600-44109800	Strong transcription	HMEC	breast
47	chr6:44102600-44119000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr6:44102800-44112000	Strong transcription	Brain Cingulate Gyrus	brain
49	chr6:44102800-44112200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr6:44103000-44108200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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