Variant report

Variant	rs7532935
Chromosome Location	chr1:151210789-151210790
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	NFIC	chr1:151210630-151211323	SK-N-SH	brain:	n/a	n/a
2	FOSL2	chr1:151210618-151211321	SK-N-SH	brain:	n/a	n/a
3	TCF12	chr1:151210611-151211455	SK-N-SH	brain:	n/a	n/a
4	EP300	chr1:151210609-151211398	SK-N-SH	brain:	n/a	n/a
5	JUND	chr1:151210678-151211382	SK-N-SH	brain:	n/a	chr1:151211046-151211057
6	RAD21	chr1:151210756-151211140	IMR90	lung:	n/a	n/a
7	SPI1	chr1:151210198-151211079	GM12878	blood:	n/a	chr1:151210589-151210598 chr1:151210587-151210600 chr1:151210585-151210594 chr1:151210469-151210476
8	FOSL2	chr1:151210743-151211285	A549	lung:	n/a	n/a
9	RUNX3	chr1:151210358-151210791	GM12878	blood:	n/a	n/a
10	TCF12	chr1:151210502-151211454	SK-N-SH	brain:	n/a	n/a
11	FOSL2	chr1:151210719-151211314	SK-N-SH	brain:	n/a	n/a
12	MXI1	chr1:151210521-151211455	IMR90	lung:	n/a	n/a
13	PBX3	chr1:151210700-151211243	SK-N-SH	brain:	n/a	n/a
14	NFIC	chr1:151210452-151210821	GM12878	blood:	n/a	n/a
15	IRF4	chr1:151210335-151210825	GM12878	blood:	n/a	n/a
16	JUND	chr1:151210672-151211307	SK-N-SH	brain:	n/a	chr1:151211046-151211057
17	JUND	chr1:151210319-151211423	SK-N-SH	brain:	n/a	chr1:151211046-151211057
18	PBX3	chr1:151210702-151211263	SK-N-SH	brain:	n/a	n/a
19	SPI1	chr1:151210352-151210800	GM12891	blood:	n/a	chr1:151210589-151210598 chr1:151210587-151210600 chr1:151210585-151210594 chr1:151210469-151210476
20	BHLHE40	chr1:151210661-151210856	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:151209513..151214380-chr1:151215209..151220595,6	MCF-7	breast:
2	chr1:151204398..151206964-chr1:151210354..151212830,2	K562	blood:
3	1:151203965-151215310..1:151402394-151411623	GM12878	blood:
4	chr1:151210527..151213187-chr1:151216256..151217892,2	K562	blood:
5	chr1:151142755..151144595-chr1:151209312..151211204,2	MCF-7	breast:
6	1:151171193-151178589..1:151203965-151215310	GM12878	blood:
7	1:151203965-151215310..1:151592347-151603110	Hela-S3	cervix:

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

Extended variants
information (count: 75 )
Associated
traits (count: 7 )

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];0.94[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];0.80[MKK][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];0.81[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];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]
rs6686402	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]
rs6695344	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][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];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];0.81[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7532935	SELENBP1	cis	cerebellum	SCAN
rs7532935	PSMD4	cis	parietal	SCAN
rs7532935	ARNT	cis	parietal	SCAN
rs7532935	PSMD4	cis	cerebellum	SCAN
rs7532935	FLG	cis	cerebellum	SCAN
rs7532935	CTSS	cis	cerebellum	SCAN
rs7532935	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	chr1:151178200-151223400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:151189600-151223600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:151190400-151223200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr1:151190400-151223400	Strong transcription	Fetal Thymus	thymus
7	chr1:151191800-151223000	Strong transcription	Fetal Stomach	stomach
8	chr1:151193400-151223000	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr1:151194400-151223600	Strong transcription	Fetal Muscle Trunk	muscle
10	chr1:151195000-151223000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:151195200-151227200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:151195600-151223000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr1:151195600-151223200	Strong transcription	Placenta	Placenta
14	chr1:151196000-151223200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:151196200-151222800	Strong transcription	Thymus	Thymus
16	chr1:151196200-151223200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr1:151196600-151222600	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr1:151196600-151223200	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr1:151196800-151222800	Strong transcription	Fetal Muscle Leg	muscle
20	chr1:151197000-151222800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:151197000-151222800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr1:151197000-151223000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:151197200-151223200	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr1:151197400-151223200	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr1:151197400-151223600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:151199200-151222600	Strong transcription	Dnd41	blood
27	chr1:151199200-151223000	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr1:151199400-151222400	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr1:151199400-151222600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr1:151199400-151222600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr1:151199400-151223000	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:151199400-151223200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:151199600-151213200	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr1:151199600-151222200	Strong transcription	HepG2	liver
35	chr1:151199600-151222400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr1:151199600-151222400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:151199600-151223200	Strong transcription	Liver	Liver
38	chr1:151199600-151223400	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr1:151199800-151213400	Strong transcription	HUVEC	blood vessel
40	chr1:151199800-151218800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr1:151199800-151222400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr1:151199800-151222400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr1:151199800-151223000	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:151199800-151223200	Strong transcription	Adipose Nuclei	Adipose
45	chr1:151200200-151213400	Strong transcription	Ovary	ovary
46	chr1:151200400-151213200	Strong transcription	Aorta	Aorta
47	chr1:151201400-151223200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr1:151202200-151222400	Strong transcription	Stomach Smooth Muscle	stomach
49	chr1:151202400-151217200	Strong transcription	Brain Germinal Matrix	brain
50	chr1:151202400-151221800	Strong transcription	Hela-S3	cervix

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