Variant report

Variant	rs3747807
Chromosome Location	chr7:86800351-86800352
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:86785879..86788454-chr7:86799611..86801663,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10085726	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10228392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10231010	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10238917	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10244350	0.88[CEU][hapmap]
rs1024457	1.00[CEU][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10245036	0.82[GIH][hapmap]
rs10257953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10273853	0.89[CEU][hapmap]
rs1058972	0.85[GIH][hapmap]
rs10952896	1.00[CEU][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2057984	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs2074757	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2106951	0.85[ASW][hapmap]
rs2108271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2108272	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2190424	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2286268	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2373387	0.92[ASW][hapmap];1.00[CEU][hapmap];0.85[TSI][hapmap];0.95[EUR][1000 genomes]
rs2373388	1.00[CEU][hapmap];0.82[YRI][hapmap];0.95[EUR][1000 genomes]
rs3789251	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789252	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4140847	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4400318	0.87[EUR][1000 genomes]
rs4639442	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4727146	0.87[EUR][1000 genomes]
rs4728686	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4728689	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4728690	0.88[GIH][hapmap];0.94[MEX][hapmap];0.91[AMR][1000 genomes]
rs6465093	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6465101	0.87[EUR][1000 genomes]
rs6952384	0.87[EUR][1000 genomes]
rs6966613	0.92[AMR][1000 genomes]
rs6968640	0.89[CEU][hapmap]
rs6975202	0.87[EUR][1000 genomes]
rs757961	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs765968	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7780698	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7800541	0.85[GIH][hapmap]
rs7810647	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs886787	1.00[CEU][hapmap];0.80[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025277	chr7:86299224-87206007	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv538999	chr7:86299224-87206007	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv532147	chr7:86299225-87121975	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	nsv1015870	chr7:86490491-86802320	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
5	nsv539000	chr7:86490491-86802320	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
6	nsv527889	chr7:86496042-86832603	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv1016761	chr7:86758544-86914152	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
8	nsv888676	chr7:86781423-86858824	Active TSS Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
9	nsv1026193	chr7:86790391-86856448	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv539003	chr7:86790391-86856448	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3747807	C7orf23	cis	parietal	SCAN
rs3747807	PCLO	cis	cerebellum	SCAN
rs3747807	SLC25A40	cis	cerebellum	SCAN
rs3747807	C7orf23	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:86782600-86811400	Weak transcription	Spleen	Spleen
2	chr7:86782800-86810800	Weak transcription	Esophagus	oesophagus
3	chr7:86782800-86811400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr7:86783000-86834000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr7:86785600-86813400	Weak transcription	Stomach Mucosa	stomach
6	chr7:86785600-86822600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr7:86786000-86801200	Weak transcription	Fetal Intestine Small	intestine
8	chr7:86786600-86828400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:86788600-86830400	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr7:86788600-86832400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr7:86789000-86832400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr7:86789000-86832400	Strong transcription	Dnd41	blood
13	chr7:86789400-86830800	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr7:86789600-86832400	Strong transcription	Fetal Thymus	thymus
15	chr7:86789800-86833000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr7:86790000-86811400	Weak transcription	Pancreas	Pancrea
17	chr7:86791000-86831600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr7:86791200-86829400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr7:86791400-86803600	Strong transcription	Fetal Muscle Leg	muscle
20	chr7:86791400-86807200	Strong transcription	Osteobl	bone
21	chr7:86791400-86807800	Strong transcription	Primary B cells from peripheral blood	blood
22	chr7:86791400-86809200	Strong transcription	K562	blood
23	chr7:86791400-86819800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr7:86791400-86830000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr7:86791400-86831800	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr7:86791400-86831800	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr7:86791600-86810800	Weak transcription	Small Intestine	intestine
28	chr7:86791600-86830600	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr7:86791600-86830600	Strong transcription	NHDF-Ad	bronchial
30	chr7:86791800-86805200	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr7:86791800-86831000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr7:86792000-86817600	Strong transcription	Primary hematopoietic stem cells	blood
33	chr7:86792000-86829200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr7:86792400-86806200	Strong transcription	HSMM	muscle
35	chr7:86792400-86807800	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr7:86792400-86827200	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr7:86792400-86828600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr7:86792400-86828600	Strong transcription	HUVEC	blood vessel
39	chr7:86792400-86829800	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr7:86792400-86831600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr7:86792600-86803200	Strong transcription	Fetal Muscle Trunk	muscle
42	chr7:86792600-86803600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr7:86792600-86803800	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr7:86792600-86804000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr7:86792600-86805000	Strong transcription	Left Ventricle	heart
46	chr7:86792600-86805800	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr7:86792600-86806200	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr7:86792600-86806400	Strong transcription	Duodenum Mucosa	Duodenum
49	chr7:86792600-86807400	Strong transcription	Placenta	Placenta
50	chr7:86792600-86808000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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