Variant report

Variant	rs2906721
Chromosome Location	chr7:101466998-101466999
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:101465557..101467704-chr7:101499795..101501367,2	K562	blood:
2	chr7:101464818..101467141-chr7:101471614..101474265,2	K562	blood:
3	chr7:101456865..101462678-chr7:101466062..101470276,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257923	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10270083	0.96[GIH][hapmap];1.00[JPT][hapmap]
rs2906717	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2906719	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2906741	0.82[AMR][1000 genomes]
rs2906743	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2906745	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2906746	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2906747	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2906748	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970461	0.96[EUR][1000 genomes]
rs2970462	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970463	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970464	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970465	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970466	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970467	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970469	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970470	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970495	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs4236558	0.92[GIH][hapmap];1.00[JPT][hapmap]
rs4354243	1.00[JPT][hapmap]
rs73183694	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933653	chr7:100701931-101515782	Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv824243	chr7:101445202-101479651	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv521041	chr7:101458144-101496391	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2906721	ARPC1B	cis	cerebellum	SCAN
rs2906721	ACHE	cis	lymphoblastoid	seeQTL
rs2906721	NAPEPLD	cis	parietal	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101461200-101468600	Weak transcription	Spleen	Spleen
2	chr7:101461200-101469800	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr7:101461200-101471800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr7:101461200-101475200	Weak transcription	Esophagus	oesophagus
5	chr7:101461200-101475400	Weak transcription	Colonic Mucosa	Colon
6	chr7:101461200-101475400	Weak transcription	Gastric	stomach
7	chr7:101461200-101486200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr7:101461400-101468400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr7:101461400-101468600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr7:101461400-101468600	Weak transcription	Ovary	ovary
11	chr7:101461400-101470600	Weak transcription	NHLF	lung
12	chr7:101461400-101471400	Weak transcription	Primary T cells from cord blood	blood
13	chr7:101461400-101473000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr7:101461600-101469800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr7:101461800-101477000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr7:101461800-101489200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr7:101462000-101468200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr7:101462000-101469400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr7:101462000-101470200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr7:101462000-101477000	Weak transcription	Brain Hippocampus Middle	brain
21	chr7:101462200-101468200	Weak transcription	Primary B cells from peripheral blood	blood
22	chr7:101462200-101468600	Weak transcription	Fetal Stomach	stomach
23	chr7:101462200-101470200	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr7:101462200-101472600	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr7:101462200-101473200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr7:101462200-101482200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr7:101462200-101484200	Weak transcription	Fetal Kidney	kidney
28	chr7:101462400-101468200	Weak transcription	Right Atrium	heart
29	chr7:101462400-101468400	Weak transcription	Fetal Intestine Large	intestine
30	chr7:101462400-101468600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr7:101462400-101468800	Weak transcription	Lung	lung
32	chr7:101462400-101470400	Weak transcription	Duodenum Mucosa	Duodenum
33	chr7:101462400-101474200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr7:101462600-101471400	Weak transcription	Osteobl	bone
35	chr7:101462800-101471800	Weak transcription	Primary B cells from cord blood	blood
36	chr7:101462800-101471800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr7:101463200-101468200	Weak transcription	Thymus	Thymus
38	chr7:101463200-101468600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr7:101463200-101471000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr7:101463600-101468600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr7:101463800-101489800	Weak transcription	NHEK	skin
42	chr7:101464200-101467200	Strong transcription	Fetal Intestine Small	intestine
43	chr7:101464400-101468200	Weak transcription	HepG2	liver
44	chr7:101464400-101468800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr7:101464400-101469400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr7:101464400-101472000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr7:101464400-101478400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr7:101464600-101467200	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr7:101464600-101468000	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr7:101464600-101468200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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