Variant report

Variant	rs6686402
Chromosome Location	chr1:151207334-151207335
allele	C/T
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	CEBPB	chr1:151207198-151207382	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	1:151203965-151215310..1:151402394-151411623	GM12878	blood:
2	chr1:150485975..150488334-chr1:151205164..151207735,2	K562	blood:
3	chr1:151206751..151209661-chr1:151226917..151228541,2	MCF-7	breast:
4	1:151171193-151178589..1:151203965-151215310	GM12878	blood:
5	1:151203965-151215310..1:151592347-151603110	Hela-S3	cervix:

Variant related genes	Relation type
PIP5K1A	TF binding region
ENSG00000159352	Chromatin interaction
ENSG00000143398	Chromatin interaction
ENSG00000238711	Chromatin interaction
ENSG00000206635	Chromatin interaction
ENSG00000228126	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1056847	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs10749660	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[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10788801	0.90[JPT][hapmap]
rs10788803	0.85[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.82[ASN][1000 genomes]
rs10888406	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10888408	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10888409	0.85[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs10888410	0.90[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs11204785	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11204791	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11204795	0.86[ASN][1000 genomes]
rs11807075	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12022732	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12040384	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12048670	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12062719	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12080778	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12407426	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1536617	0.85[JPT][hapmap]
rs16827941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16833079	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1752387	0.81[JPT][hapmap]
rs1892196	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2025900	0.86[JPT][hapmap]
rs2031797	0.85[JPT][hapmap]
rs2275900	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2769268	0.86[JPT][hapmap]
rs2769273	0.86[JPT][hapmap]
rs2800946	0.86[JPT][hapmap]
rs3811405	0.86[GIH][hapmap];0.90[JPT][hapmap]
rs3811406	0.85[JPT][hapmap]
rs41302131	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4246525	0.90[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap]
rs4291501	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4520422	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[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4522000	0.80[ASN][1000 genomes]
rs4636463	0.90[GIH][hapmap];0.85[JPT][hapmap]
rs4970944	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4970948	0.90[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs4971013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4971015	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4971016	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4971018	0.85[JPT][hapmap]
rs4971021	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4971023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4971025	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4971026	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4971027	0.90[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.84[ASN][1000 genomes]
rs4971029	0.85[JPT][hapmap]
rs4971030	0.90[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs5022636	0.81[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap]
rs58323986	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61817972	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6587559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587562	0.95[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6678528	0.90[JPT][hapmap]
rs6681071	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6681163	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6683396	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6695344	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6701325	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521064	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7527032	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];1.00[ASN][1000 genomes]
rs7532935	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];0.93[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];1.00[ASN][1000 genomes]
rs7539584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7544947	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7545392	0.90[JPT][hapmap]
rs7552906	0.86[JPT][hapmap]
rs943637	0.90[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][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	nsv831559	chr1:151109459-151239921	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv831570	chr1:151129020-151281778	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	106 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6686402	SELENBP1	cis	cerebellum	SCAN
rs6686402	ARNT	cis	parietal	SCAN
rs6686402	FLG	cis	cerebellum	SCAN
rs6686402	PSMD4	cis	parietal	SCAN
rs6686402	ANKRD34A	cis	cerebellum	SCAN
rs6686402	CTSS	cis	cerebellum	SCAN
rs6686402	PSMD4	cis	cerebellum	SCAN
rs6686402	MRPS21	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151173200-151212000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:151173200-151227200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:151173600-151210600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:151178200-151223400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:151186800-151210000	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr1:151189600-151223600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:151190400-151223200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr1:151190400-151223400	Strong transcription	Fetal Thymus	thymus
9	chr1:151191800-151223000	Strong transcription	Fetal Stomach	stomach
10	chr1:151193400-151223000	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr1:151194400-151223600	Strong transcription	Fetal Muscle Trunk	muscle
12	chr1:151194600-151208800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:151194800-151210000	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr1:151195000-151209000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:151195000-151223000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:151195200-151227200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr1:151195400-151209800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:151195600-151223000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr1:151195600-151223200	Strong transcription	Placenta	Placenta
20	chr1:151195800-151210000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:151196000-151223200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:151196200-151210200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:151196200-151222800	Strong transcription	Thymus	Thymus
24	chr1:151196200-151223200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr1:151196600-151222600	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr1:151196600-151223200	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr1:151196800-151222800	Strong transcription	Fetal Muscle Leg	muscle
28	chr1:151197000-151222800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:151197000-151222800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:151197000-151223000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:151197200-151223200	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr1:151197400-151223200	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr1:151197400-151223600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:151197600-151209400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:151199000-151210200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:151199200-151222600	Strong transcription	Dnd41	blood
37	chr1:151199200-151223000	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr1:151199400-151208400	Strong transcription	A549	lung
39	chr1:151199400-151209800	Strong transcription	Primary B cells from peripheral blood	blood
40	chr1:151199400-151209800	Strong transcription	Osteobl	bone
41	chr1:151199400-151222400	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr1:151199400-151222600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr1:151199400-151222600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr1:151199400-151223000	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr1:151199400-151223200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr1:151199600-151210000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:151199600-151210000	Strong transcription	NH-A	brain
48	chr1:151199600-151213200	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr1:151199600-151222200	Strong transcription	HepG2	liver
50	chr1:151199600-151222400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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