Variant report

Variant	rs651717
Chromosome Location	chr1:70608053-70608054
allele	A/C
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	CTCF	chr1:70607912-70608081	MCF-7	breast:	n/a	chr1:70607992-70608008
2	CTCF	chr1:70607920-70608070	HFF	foreskin:	n/a	chr1:70607992-70608008
3	CTCF	chr1:70607940-70608090	HBMEC	blood vessel:	n/a	chr1:70607992-70608008
4	CTCF	chr1:70608020-70608170	RPTEC	kidney:	n/a	n/a
5	CTCF	chr1:70607940-70608090	NHDF-neo	bronchial:	n/a	chr1:70607992-70608008
6	RAD21	chr1:70607854-70608151	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr1:70607920-70608070	HMEC	breast:	n/a	chr1:70607992-70608008
8	CTCF	chr1:70607980-70608130	HEEpiC	esophagus:	n/a	chr1:70607992-70608008
9	CTCF	chr1:70607920-70608070	HPF	lung:	n/a	chr1:70607992-70608008
10	CTCF	chr1:70607920-70608070	HCFaa	heart:	n/a	chr1:70607992-70608008
11	CTCF	chr1:70607940-70608090	NHLF	lung:	n/a	chr1:70607992-70608008
12	CTCF	chr1:70607820-70608201	IMR90	lung:	n/a	chr1:70607992-70608008
13	CTCF	chr1:70607719-70608360	SK-N-SH	brain:	n/a	chr1:70607992-70608008
14	RAD21	chr1:70607865-70608058	SK-N-SH_RA	brain:	n/a	n/a
15	RAD21	chr1:70607774-70608135	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr1:70607980-70608130	GM06990	blood:	n/a	chr1:70607992-70608008
17	RAD21	chr1:70607857-70608108	MCF-7	breast:	n/a	n/a
18	CTCF	chr1:70607940-70608090	GM12874	blood:	n/a	chr1:70607992-70608008
19	CTCF	chr1:70607969-70608061	HepG2	liver:	n/a	chr1:70607992-70608008
20	CTCF	chr1:70607962-70608060	Kidney_OC	kidney:	n/a	chr1:70607992-70608008
21	CTCF	chr1:70607920-70608070	GM06990	blood:	n/a	chr1:70607992-70608008
22	RAD21	chr1:70607811-70608167	IMR90	lung:	n/a	n/a
23	RAD21	chr1:70607681-70608322	SK-N-SH	brain:	n/a	n/a
24	CTCF	chr1:70607960-70608110	HRPEpiC	eye:	n/a	chr1:70607992-70608008
25	CTCF	chr1:70607960-70608110	NHDF-neo	bronchial:	n/a	chr1:70607992-70608008
26	CTCF	chr1:70607924-70608064	LNCaP	prostate:	n/a	chr1:70607992-70608008
27	CTCF	chr1:70607960-70608110	HCPEpiC	choroid plexus:	n/a	chr1:70607992-70608008
28	CTCF	chr1:70607940-70608090	AG10803	skin:	n/a	chr1:70607992-70608008
29	CTCF	chr1:70607920-70608070	HMF	breast:	n/a	chr1:70607992-70608008
30	CTCF	chr1:70607910-70608069	Gliobla	brain:	n/a	chr1:70607992-70608008
31	CTCF	chr1:70607932-70608096	Pancreas_OC	pancreas:	n/a	chr1:70607992-70608008
32	CTCF	chr1:70607920-70608070	AG04450	lung:	n/a	chr1:70607992-70608008
33	CTCF	chr1:70607940-70608090	HPF	lung:	n/a	chr1:70607992-70608008
34	CTCF	chr1:70607960-70608110	AG09319	gingival:	n/a	chr1:70607992-70608008
35	CTCF	chr1:70607920-70608070	SAEC	small airway:	n/a	chr1:70607992-70608008
36	CTCF	chr1:70607929-70608060	Medullo	brain:	n/a	chr1:70607992-70608008
37	CTCF	chr1:70607908-70608108	Hela-S3	cervix:	n/a	chr1:70607992-70608008
38	SMC3	chr1:70607709-70608215	SK-N-SH	brain:	n/a	n/a
39	CTCF	chr1:70607920-70608070	AoAF	blood vessel:	n/a	chr1:70607992-70608008
40	CTCF	chr1:70607906-70608079	HUVEC	blood vessel:	n/a	chr1:70607992-70608008
41	CTCF	chr1:70607940-70608090	HPAF	blood vessel:	n/a	chr1:70607992-70608008
42	CTCF	chr1:70607906-70608111	K562	blood:	n/a	chr1:70607992-70608008
43	CTCF	chr1:70607798-70608179	K562	blood:	n/a	chr1:70607992-70608008
44	CTCF	chr1:70608020-70608170	AG04450	lung:	n/a	n/a
45	CTCF	chr1:70607940-70608090	HCPEpiC	choroid plexus:	n/a	chr1:70607992-70608008
46	RAD21	chr1:70607869-70608134	Hela-S3	cervix:	n/a	n/a
47	CTCF	chr1:70607920-70608070	AG04449	skin:	n/a	chr1:70607992-70608008
48	RAD21	chr1:70607814-70608114	MCF-7	breast:	n/a	n/a
49	CTCF	chr1:70607769-70608245	MCF-7	breast:	n/a	chr1:70607992-70608008
50	CTCF	chr1:70607940-70608090	HEEpiC	esophagus:	n/a	chr1:70607992-70608008

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:70607998..70610574-chr1:70685135..70686722,2	K562	blood:
2	chr1:70606579..70609498-chr1:70685222..70687844,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRRC7-1	chr1:70607065-70610047	ENSG00000261223.1

Variant related genes	Relation type
LRRC7	TF binding region
ENSG00000116754	Chromatin interaction
ENSG00000228988	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1412867	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17131236	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17131238	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17131241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34121744	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35522955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3753818	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs476591	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs522320	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs549843	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56299138	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56873377	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57098486	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs587567	1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60409157	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60598073	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs610953	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61785267	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61785269	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61785270	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61785272	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs632047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs666163	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6664084	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6664480	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6666941	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6700543	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs676753	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74085998	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7533067	0.89[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.87[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	nsv531879	chr1:70386455-70644617	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1005397	chr1:70598803-70634585	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	esv1796744	chr1:70604106-70621290	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	esv1798518	chr1:70604106-70723347	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv1797140	chr1:70604106-70724622	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv871339	chr1:70605735-70634463	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs651717	WLS	cis	cerebellum	SCAN
rs651717	SFRS11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70596800-70609200	Weak transcription	Liver	Liver
2	chr1:70599000-70609600	Weak transcription	GM12878-XiMat	blood
3	chr1:70601000-70615400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr1:70601000-70643200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr1:70601200-70652000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr1:70603000-70614800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:70603400-70648800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:70604600-70608600	Enhancers	Fetal Lung	lung
9	chr1:70605200-70612200	Weak transcription	Primary B cells from cord blood	blood
10	chr1:70605400-70608200	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr1:70605400-70639400	Weak transcription	Brain Anterior Caudate	brain
12	chr1:70605800-70608800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:70605800-70609200	Enhancers	NHDF-Ad	bronchial
14	chr1:70605800-70609200	Enhancers	NHLF	lung
15	chr1:70605800-70609600	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr1:70606000-70608200	Enhancers	Rectal Smooth Muscle	rectum
17	chr1:70606200-70610600	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr1:70606400-70608400	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr1:70606400-70609800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:70606400-70611200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:70606400-70612200	Weak transcription	Primary T cells from cord blood	blood
22	chr1:70606600-70608800	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr1:70606600-70609200	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr1:70606600-70610200	Weak transcription	NH-A	brain
25	chr1:70606600-70611400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr1:70606600-70611800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr1:70606600-70612800	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr1:70606600-70614800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr1:70606600-70617600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr1:70606600-70619600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:70606600-70629600	Weak transcription	Fetal Intestine Small	intestine
32	chr1:70606600-70633800	Weak transcription	Fetal Intestine Large	intestine
33	chr1:70606800-70608400	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr1:70606800-70609200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:70606800-70609200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:70606800-70609400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:70606800-70610400	Weak transcription	Fetal Heart	heart
38	chr1:70606800-70612800	Weak transcription	Fetal Kidney	kidney
39	chr1:70606800-70617000	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr1:70606800-70627800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:70606800-70634800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr1:70606800-70634800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr1:70606800-70651600	Weak transcription	Stomach Smooth Muscle	stomach
44	chr1:70606800-70661800	Weak transcription	Brain Hippocampus Middle	brain
45	chr1:70607000-70609200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:70607000-70609400	Enhancers	Fetal Brain Male	brain
47	chr1:70607000-70609600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:70607000-70609600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:70607000-70610200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr1:70607000-70611400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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