Variant report

Variant	rs2906648
Chromosome Location	chr7:101571083-101571084
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr7:101570388-101571183	MCF-7	breast:	n/a	chr7:101570880-101570891 chr7:101570636-101570653
2	CEBPB	chr7:101570681-101571122	A549	lung:	n/a	chr7:101570880-101570891
3	FOXP2	chr7:101571044-101571353	PFSK-1	brain:	n/a	n/a
4	FOXA2	chr7:101571039-101571372	A549	lung:	n/a	n/a
5	CEBPB	chr7:101570782-101571135	A549	lung:	n/a	chr7:101570880-101570891

No.	Distal block	Cell Line	Cell type
1	chr7:101568916..101572896-chr7:101575623..101579716,5	K562	blood:
2	chr7:101570061..101571761-chr7:101572477..101575327,2	K562	blood:
3	chr7:101563285..101566884-chr7:101569000..101572598,3	MCF-7	breast:
4	chr7:101569775..101571277-chr7:101578145..101580741,2	MCF-7	breast:

Variant related genes	Relation type
CUX1	TF binding region
ENSG00000257923	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11977398	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2906652	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs2906654	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2906655	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2906656	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs4727512	1.00[YRI][hapmap];0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024319	chr7:101368299-101668159	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv539047	chr7:101368299-101668159	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1020372	chr7:101420819-101718950	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv482846	chr7:101539981-101707666	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv888827	chr7:101562674-101650302	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2906648	C7orf61	cis	parietal	SCAN
rs2906648	ARPC1B	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101544200-101579800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:101556000-101572600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr7:101557400-101573600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr7:101557600-101571200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr7:101558600-101577800	Weak transcription	Brain Angular Gyrus	brain
6	chr7:101560000-101577000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr7:101561200-101584000	Weak transcription	Hela-S3	cervix
8	chr7:101561400-101572600	Weak transcription	GM12878-XiMat	blood
9	chr7:101561600-101575200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr7:101561600-101577600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr7:101561800-101571200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr7:101561800-101574800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr7:101561800-101577400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr7:101561800-101579200	Weak transcription	NHEK	skin
15	chr7:101562000-101578000	Weak transcription	Colonic Mucosa	Colon
16	chr7:101562000-101583600	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr7:101562600-101575400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr7:101562800-101573400	Weak transcription	Primary B cells from peripheral blood	blood
19	chr7:101562800-101578200	Weak transcription	Fetal Kidney	kidney
20	chr7:101563000-101577200	Weak transcription	Duodenum Mucosa	Duodenum
21	chr7:101563000-101578800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr7:101563200-101571200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr7:101563200-101571200	Weak transcription	Adipose Nuclei	Adipose
24	chr7:101563200-101573000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr7:101563200-101577800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr7:101563400-101573600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr7:101563400-101578600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr7:101566200-101579000	Weak transcription	Spleen	Spleen
29	chr7:101566400-101577800	Weak transcription	Gastric	stomach
30	chr7:101566400-101577800	Weak transcription	Lung	lung
31	chr7:101566600-101577200	Weak transcription	Fetal Lung	lung
32	chr7:101566800-101571400	Strong transcription	Fetal Intestine Small	intestine
33	chr7:101567000-101577000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr7:101567000-101578000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr7:101567000-101596000	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr7:101567200-101572600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr7:101567200-101574000	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr7:101567200-101577200	Weak transcription	Ovary	ovary
39	chr7:101567200-101577200	Weak transcription	Stomach Mucosa	stomach
40	chr7:101567200-101577800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr7:101567200-101579200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr7:101567400-101574800	Weak transcription	Right Ventricle	heart
43	chr7:101567600-101572600	Weak transcription	Fetal Thymus	thymus
44	chr7:101567600-101577200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr7:101567600-101577200	Weak transcription	Aorta	Aorta
46	chr7:101567600-101577800	Weak transcription	Fetal Muscle Leg	muscle
47	chr7:101567600-101577800	Weak transcription	NHLF	lung
48	chr7:101567800-101573600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr7:101567800-101574200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr7:101567800-101577200	Weak transcription	HSMMtube	muscle

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