Variant report

Variant	rs391234
Chromosome Location	chr7:101694275-101694276
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	chr7:101688104..101690930-chr7:101693641..101697108,3	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10231704	1.00[CHD][hapmap]
rs10245459	1.00[CHD][hapmap]
rs10246310	1.00[CHD][hapmap]
rs10249739	1.00[CHD][hapmap]
rs10252737	1.00[CHD][hapmap]
rs382270	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs388781	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs392438	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs401301	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs401966	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs411656	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs421168	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs424478	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs425934	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs436483	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs450854	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7796231	0.88[AMR][1000 genomes];0.86[EUR][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	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
2	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
3	nsv482521	chr7:101604002-101718950	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv831080	chr7:101629121-101718950	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1027574	chr7:101654060-101718950	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv607985	chr7:101683563-101718950	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs391234	CUX1	cis	cerebellum	SCAN
rs391234	RINT1	cis	cerebellum	SCAN
rs391234	PTCD1	cis	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101642800-101697600	Weak transcription	Primary B cells from cord blood	blood
2	chr7:101668000-101707200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr7:101672200-101697000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr7:101672400-101697200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr7:101674200-101707400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr7:101674400-101696800	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr7:101674400-101697000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr7:101679000-101695200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr7:101684200-101697400	Weak transcription	Liver	Liver
10	chr7:101685600-101697200	Weak transcription	HepG2	liver
11	chr7:101688400-101697000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr7:101688400-101706400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr7:101688600-101707200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:101689000-101695200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr7:101689400-101697400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr7:101689400-101706400	Weak transcription	Stomach Mucosa	stomach
17	chr7:101689400-101714600	Weak transcription	HSMMtube	muscle
18	chr7:101689600-101696600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr7:101689800-101694600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr7:101689800-101714800	Weak transcription	NHLF	lung
21	chr7:101690000-101704600	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr7:101690200-101696600	Weak transcription	Fetal Muscle Leg	muscle
23	chr7:101690200-101705000	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr7:101690400-101704600	Weak transcription	Spleen	Spleen
25	chr7:101690400-101704800	Weak transcription	Placenta	Placenta
26	chr7:101690600-101713800	Weak transcription	Fetal Lung	lung
27	chr7:101690600-101713800	Weak transcription	Ovary	ovary
28	chr7:101691000-101694400	Enhancers	Fetal Heart	heart
29	chr7:101691200-101694400	Weak transcription	A549	lung
30	chr7:101692600-101694400	Enhancers	Right Atrium	heart
31	chr7:101692800-101694400	Enhancers	Left Ventricle	heart
32	chr7:101692800-101695800	Weak transcription	Dnd41	blood
33	chr7:101693000-101694400	Enhancers	Right Ventricle	heart
34	chr7:101693000-101696600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr7:101693200-101696800	Weak transcription	Primary hematopoietic stem cells	blood
36	chr7:101693200-101696800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr7:101693200-101696800	Weak transcription	Fetal Intestine Small	intestine
38	chr7:101693400-101695800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr7:101693400-101696400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr7:101693400-101697200	Weak transcription	Thymus	Thymus
41	chr7:101693400-101697600	Weak transcription	Fetal Stomach	stomach
42	chr7:101693400-101704600	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr7:101693600-101695000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr7:101693600-101697200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr7:101693800-101697600	Weak transcription	Fetal Intestine Large	intestine
46	chr7:101694000-101694400	Strong transcription	Primary T cells from cord blood	blood
47	chr7:101694000-101694600	Enhancers	GM12878-XiMat	blood
48	chr7:101694000-101694800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr7:101694000-101695000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr7:101694000-101695000	Enhancers	Fetal Thymus	thymus

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