Variant report

Variant	rs4971007
Chromosome Location	chr1:151108137-151108138
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:63)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:151108020-151108170	GM12872	blood:	n/a	n/a
2	CTCF	chr1:151108036-151108228	GM12892	blood:	n/a	n/a
3	RUNX3	chr1:151108131-151108612	GM12878	blood:	n/a	n/a
4	CTCF	chr1:151108060-151108210	WERI-Rb-1	eye:	n/a	n/a
5	CTCF	chr1:151107878-151108269	K562	blood:	n/a	n/a
6	RAD21	chr1:151107972-151108236	HepG2	liver:	n/a	n/a
7	CTCF	chr1:151108020-151108170	A549	lung:	n/a	n/a
8	CTCF	chr1:151108131-151108150	GM10266	blood:	n/a	n/a
9	CTCF	chr1:151108041-151108239	MCF-7	breast:	n/a	n/a
10	CTCF	chr1:151108040-151108190	GM12872	blood:	n/a	n/a
11	CTCF	chr1:151108120-151108270	HBMEC	blood vessel:	n/a	n/a
12	CTCF	chr1:151108042-151108244	GM19239	blood:	n/a	n/a
13	CTCF	chr1:151108008-151108255	GM19238	blood:	n/a	n/a
14	CTCF	chr1:151108042-151108231	MCF-7	breast:	n/a	n/a
15	RUNX3	chr1:151108137-151108608	GM12878	blood:	n/a	n/a
16	CTCF	chr1:151108100-151108250	HFF	foreskin:	n/a	n/a
17	CTCF	chr1:151108040-151108190	GM12875	blood:	n/a	n/a
18	CTCF	chr1:151108030-151108193	GM19240	blood:	n/a	n/a
19	CTCF	chr1:151108039-151108229	GM12891	blood:	n/a	n/a
20	CTCF	chr1:151108100-151108250	HEK293	kidney:	n/a	n/a
21	CTCF	chr1:151108020-151108170	HepG2	liver:	n/a	n/a
22	CTCF	chr1:151107999-151108267	K562	blood:	n/a	n/a
23	CTCF	chr1:151108100-151108250	K562	blood:	n/a	n/a
24	CTCF	chr1:151108046-151108191	HUVEC	blood vessel:	n/a	n/a
25	CTCF	chr1:151108080-151108230	GM12872	blood:	n/a	n/a
26	CTCF	chr1:151108100-151108250	WERI-Rb-1	eye:	n/a	n/a
27	CTCF	chr1:151108060-151108210	RPTEC	kidney:	n/a	n/a
28	CTCF	chr1:151108032-151108246	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr1:151107990-151108210	HepG2	liver:	n/a	n/a
30	CTCF	chr1:151108009-151108216	H1-hESC	embryonic stem cell:	n/a	n/a
31	CTCF	chr1:151108054-151108226	MCF-7	breast:	n/a	n/a
32	CTCF	chr1:151108100-151108250	NB4	blood:	n/a	n/a
33	CTCF	chr1:151108060-151108210	GM12866	blood:	n/a	n/a
34	CTCF	chr1:151108040-151108190	HEK293	kidney:	n/a	n/a
35	RAD21	chr1:151108023-151108205	HepG2	liver:	n/a	n/a
36	CTCF	chr1:151108040-151108190	GM12865	blood:	n/a	n/a
37	CTCF	chr1:151107933-151108234	K562	blood:	n/a	n/a
38	CTCF	chr1:151108080-151108230	GM12874	blood:	n/a	n/a
39	CTCF	chr1:151108063-151108151	ProgFib	skin:	n/a	n/a
40	CTCF	chr1:151108047-151108216	K562	blood:	n/a	n/a
41	CTCF	chr1:151108044-151108209	GM13977	blood:	n/a	n/a
42	CTCF	chr1:151108102-151108239	GM12878	blood:	n/a	n/a
43	CTCF	chr1:151108030-151108241	MCF-7	breast:	n/a	n/a
44	CTCF	chr1:151108060-151108210	GM06990	blood:	n/a	n/a
45	UBTF	chr1:151108113-151108187	K562	blood:	n/a	n/a
46	CTCF	chr1:151108033-151108236	MCF-7	breast:	n/a	n/a
47	CTCF	chr1:151108020-151108170	Caco-2	colon:	n/a	n/a
48	CTCF	chr1:151108046-151108195	HepG2	liver:	n/a	n/a
49	POLR2A	chr1:151107967-151108441	H1-neurons	neurons:	n/a	n/a
50	CTCF	chr1:151108061-151108203	NHEK	skin:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151106109..151108676-chr1:151117941..151119953,3	K562	blood:
2	chr1:151101938..151104431-chr1:151107566..151109145,2	MCF-7	breast:
3	chr1:151106923..151108713-chr1:151252226..151254110,2	K562	blood:
4	chr1:151107806..151108623-chr1:151128265..151128961,2	K562	blood:
5	chr1:151104790..151107252-chr1:151107376..151109485,2	K562	blood:
6	chr1:151106109..151110392-chr1:151117941..151122227,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000261168	TF binding region
SEMA6C	TF binding region
ENSG00000261168	Chromatin interaction
ENSG00000143434	Chromatin interaction
ENSG00000143373	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10788798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10788799	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11204777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11204778	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11204780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11204782	1.00[JPT][hapmap]
rs11807526	1.00[JPT][hapmap]
rs12039542	0.80[EUR][1000 genomes]
rs12087892	1.00[JPT][hapmap]
rs12117163	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12569193	0.86[JPT][hapmap]
rs1524773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs15740	0.84[CEU][hapmap]
rs2067606	1.00[JPT][hapmap]
rs2140709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2902810	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap]
rs3738481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3806386	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs3806387	0.89[CEU][hapmap];0.88[CHB][hapmap]
rs4357530	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs4512652	0.86[JPT][hapmap]
rs4970939	0.82[EUR][1000 genomes]
rs4970941	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs4970993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4970998	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4970999	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4971000	0.83[EUR][1000 genomes]
rs4971002	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4971003	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4971005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4971006	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4971008	0.89[CEU][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5023311	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6587552	0.81[CHD][hapmap]
rs6587553	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap]
rs6587557	0.86[JPT][hapmap]
rs6656450	0.86[JPT][hapmap]
rs6668894	0.84[EUR][1000 genomes]
rs6674970	0.86[JPT][hapmap]
rs6676190	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs6694158	1.00[CHB][hapmap];0.81[GIH][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs7523731	1.00[JPT][hapmap]
rs7532312	1.00[CHB][hapmap]
rs7540258	1.00[CHB][hapmap]
rs7550434	1.00[CHB][hapmap]
rs7554936	1.00[JPT][hapmap]

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	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
5	nsv872422	chr1:151098077-151115186	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv872423	chr1:151100612-151115997	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs4971007	GABPB2	cis	cerebellum	SCAN
rs4971007	LYSMD1	Cis_1M	lymphoblastoid	RTeQTL
rs4971007	ZNF687	cis	cerebellum	SCAN
rs4971007	BNIPL	cis	lung	GTEx
rs4971007	PRPF3	cis	parietal	SCAN
rs4971007	RPTN	cis	cerebellum	SCAN
rs4971007	MRPS21	cis	cerebellum	SCAN
rs4971007	MRPS21	cis	parietal	SCAN
rs4971007	PGLYRP4	cis	parietal	SCAN
rs4971007	CDC42SE1	cis	parietal	SCAN
rs4971007	CDC42SE1	cis	lymphoblastoid	seeQTL

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151079800-151114800	Weak transcription	HSMM	muscle
2	chr1:151104000-151114800	Weak transcription	Psoas Muscle	Psoas
3	chr1:151104400-151110400	Weak transcription	NHLF	lung
4	chr1:151104400-151111200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:151104400-151116600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:151104400-151117000	Weak transcription	Fetal Kidney	kidney
7	chr1:151104400-151118000	Weak transcription	Aorta	Aorta
8	chr1:151104600-151108200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr1:151104600-151109000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:151104600-151117400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:151104600-151118200	Weak transcription	Primary T cells from cord blood	blood
12	chr1:151104800-151108200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:151104800-151108400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:151104800-151115600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr1:151105000-151114800	Strong transcription	Fetal Brain Female	brain
16	chr1:151105000-151114800	Weak transcription	Right Atrium	heart
17	chr1:151105000-151115400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:151105000-151115600	Weak transcription	Fetal Thymus	thymus
19	chr1:151105200-151108200	Weak transcription	Esophagus	oesophagus
20	chr1:151105200-151115200	Weak transcription	Colon Smooth Muscle	Colon
21	chr1:151105200-151115400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr1:151105200-151117000	Weak transcription	Placenta	Placenta
23	chr1:151105400-151117000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr1:151105600-151112800	Strong transcription	Left Ventricle	heart
25	chr1:151105600-151114800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:151105600-151115800	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr1:151105600-151118000	Weak transcription	Gastric	stomach
28	chr1:151105800-151113000	Strong transcription	Stomach Smooth Muscle	stomach
29	chr1:151105800-151115600	Weak transcription	Thymus	Thymus
30	chr1:151105800-151117200	Weak transcription	Spleen	Spleen
31	chr1:151106000-151109200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:151106000-151111000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
33	chr1:151106000-151112200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:151106000-151113200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:151106000-151113200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:151106000-151113400	Strong transcription	Fetal Intestine Large	intestine
37	chr1:151106000-151114800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
38	chr1:151106000-151115000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:151106200-151110600	Strong transcription	HSMMtube	muscle
40	chr1:151106200-151110800	Strong transcription	Brain Hippocampus Middle	brain
41	chr1:151106200-151110800	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr1:151106200-151113000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr1:151106200-151113000	Strong transcription	Fetal Lung	lung
44	chr1:151106200-151116000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr1:151106400-151109000	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr1:151106600-151109400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:151106600-151109600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:151106600-151109600	Strong transcription	Brain Cingulate Gyrus	brain
49	chr1:151106600-151110200	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr1:151106600-151111000	Strong transcription	Brain Anterior Caudate	brain

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