Variant report

Variant	rs6958533
Chromosome Location	chr7:102571713-102571714
allele	A/G
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	POLR2A	chr7:102571703-102571726	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
LRRC17	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10236090	0.89[AFR][1000 genomes]
rs10240915	0.90[YRI][hapmap];0.81[AFR][1000 genomes]
rs10259205	1.00[ASW][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10268849	1.00[MEX][hapmap]
rs10278727	0.89[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap]
rs10808121	0.84[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap]
rs1100047	0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11560367	1.00[MEX][hapmap]
rs12671524	1.00[AMR][1000 genomes]
rs13242079	1.00[MEX][hapmap]
rs1404213	1.00[MEX][hapmap]
rs1543987	1.00[MEX][hapmap];0.83[MKK][hapmap]
rs1916990	1.00[AMR][1000 genomes]
rs1968199	1.00[MEX][hapmap]
rs1969429	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2041949	1.00[MEX][hapmap]
rs2140621	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2177550	0.84[ASW][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[AMR][1000 genomes]
rs2193418	1.00[MEX][hapmap]
rs28393249	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2898638	1.00[ASW][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3181009	1.00[MEX][hapmap]
rs4255065	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4576360	0.89[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap]
rs4727558	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4729872	1.00[MEX][hapmap]
rs6465883	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6465888	0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap]
rs6465890	1.00[MEX][hapmap]
rs6950177	1.00[MEX][hapmap]
rs6962336	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6973115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6973702	1.00[MEX][hapmap]
rs6977206	1.00[MEX][hapmap]
rs7341515	0.93[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap]
rs7783856	1.00[MEX][hapmap]
rs7784337	1.00[MEX][hapmap]
rs7805950	0.84[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap]
rs7806136	1.00[MEX][hapmap];0.80[MKK][hapmap]
rs7806691	1.00[MEX][hapmap];0.86[MKK][hapmap]
rs7809075	0.93[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap]
rs847650	0.84[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap]
rs847653	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs847654	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs847655	1.00[AMR][1000 genomes]
rs847657	0.96[AFR][1000 genomes]
rs864709	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016563	chr7:101912320-102695860	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1028438	chr7:101912320-102704135	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	esv2752138	chr7:102358320-102787135	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv608058	chr7:102466741-102571713	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv464667	chr7:102486254-102624192	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv608060	chr7:102486254-102624192	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats 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	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102517200-102578200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr7:102566800-102573000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr7:102567200-102573200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr7:102567600-102573000	Weak transcription	Fetal Muscle Leg	muscle
5	chr7:102567600-102573600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr7:102567600-102574000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr7:102567800-102573800	Weak transcription	NHLF	lung
8	chr7:102568000-102571800	Weak transcription	Fetal Kidney	kidney
9	chr7:102568000-102573200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr7:102568200-102572000	Strong transcription	K562	blood
11	chr7:102568200-102573000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr7:102568200-102573000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr7:102568200-102573600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr7:102568400-102573000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr7:102568400-102573000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr7:102568400-102573800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr7:102568600-102572600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr7:102568600-102573000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr7:102568600-102573000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr7:102568600-102573200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr7:102568600-102573400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr7:102568600-102573800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr7:102568600-102573800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr7:102568600-102574600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr7:102568600-102574600	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr7:102568600-102574800	Weak transcription	Osteobl	bone
27	chr7:102568800-102573200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr7:102568800-102573400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr7:102569200-102572200	Genic enhancers	Fetal Lung	lung
30	chr7:102569400-102573400	Weak transcription	Brain Germinal Matrix	brain
31	chr7:102570600-102572400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr7:102570800-102571800	Strong transcription	NH-A	brain
33	chr7:102571200-102571800	Enhancers	Ovary	ovary
34	chr7:102571200-102573800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr7:102571400-102571800	Enhancers	Fetal Stomach	stomach
36	chr7:102571400-102571800	Enhancers	Gastric	stomach
37	chr7:102571400-102579600	Genic enhancers	HSMM	muscle
38	chr7:102571600-102571800	Enhancers	Left Ventricle	heart
39	chr7:102571600-102572800	Enhancers	Stomach Mucosa	stomach
40	chr7:102571600-102573200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr7:102571600-102573200	Weak transcription	HSMMtube	muscle
42	chr7:102571600-102574800	Weak transcription	Aorta	Aorta
43	chr7:102571600-102581800	Weak transcription	Fetal Intestine Small	intestine

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