Variant report

Variant	rs3811418
Chromosome Location	chr1:151805049-151805050
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	TCF7L2	chr1:151805035-151805312	Hela-S3	cervix:	n/a	n/a
2	CEBPB	chr1:151804973-151805409	Hela-S3	cervix:	n/a	n/a
3	NFIC	chr1:151804884-151805562	ECC-1	luminal epithelium:	n/a	n/a
4	GATA3	chr1:151805046-151805692	T-47D	breast:	n/a	n/a
5	MXI1	chr1:151804930-151805443	HepG2	liver:	n/a	n/a
6	MAX	chr1:151805014-151805633	ECC-1	luminal epithelium:	n/a	chr1:151805317-151805328 chr1:151805319-151805326 chr1:151805318-151805327
7	FOXA1	chr1:151805004-151805389	HepG2	liver:	n/a	n/a
8	GATA3	chr1:151804849-151805615	MCF-7	breast:	n/a	n/a
9	EP300	chr1:151805008-151805439	HepG2	liver:	n/a	chr1:151805297-151805310
10	SRF	chr1:151804879-151805417	ECC-1	luminal epithelium:	n/a	n/a
11	TBP	chr1:151804994-151805412	HepG2	liver:	n/a	n/a
12	NFIC	chr1:151804910-151805546	ECC-1	luminal epithelium:	n/a	n/a
13	YY1	chr1:151805017-151805494	HepG2	liver:	n/a	n/a
14	MAX	chr1:151804780-151805733	MCF-7	breast:	n/a	chr1:151805317-151805328 chr1:151805319-151805326 chr1:151805318-151805327
15	CEBPB	chr1:151804989-151805362	HepG2	liver:	n/a	n/a
16	MAX	chr1:151804687-151805651	HepG2	liver:	n/a	chr1:151805317-151805328 chr1:151805319-151805326 chr1:151805318-151805327
17	POLR2A	chr1:151804957-151805450	HepG2	liver:	n/a	n/a
18	MAX	chr1:151804925-151805553	Hela-S3	cervix:	n/a	chr1:151805317-151805328 chr1:151805319-151805326 chr1:151805318-151805327
19	CEBPB	chr1:151804875-151805543	MCF-7	breast:	n/a	n/a
20	CEBPB	chr1:151805016-151805354	HepG2	liver:	n/a	n/a
21	RCOR1	chr1:151805013-151805411	Hela-S3	cervix:	n/a	n/a
22	MAX	chr1:151804765-151805641	HepG2	liver:	n/a	chr1:151805317-151805328 chr1:151805319-151805326 chr1:151805318-151805327
23	NR2C2	chr1:151804173-151805354	Hela-S3	cervix:	n/a	n/a
24	EP300	chr1:151804899-151805502	T-47D	breast:	n/a	chr1:151805297-151805310
25	ZNF263	chr1:151804751-151805096	HEK293-T-REx	kidney:	n/a	n/a
26	HDAC2	chr1:151805003-151805371	HepG2	liver:	n/a	n/a
27	MAX	chr1:151805049-151805538	HCT-116	colon:	n/a	chr1:151805317-151805328 chr1:151805319-151805326 chr1:151805318-151805327
28	ZNF143	chr1:151805008-151805383	Hela-S3	cervix:	n/a	n/a
29	SRF	chr1:151804995-151805411	ECC-1	luminal epithelium:	n/a	n/a
30	MXI1	chr1:151804974-151805540	IMR90	lung:	n/a	n/a
31	CEBPB	chr1:151804964-151805363	ECC-1	luminal epithelium:	n/a	n/a
32	MAX	chr1:151805006-151805559	Hela-S3	cervix:	n/a	chr1:151805317-151805328 chr1:151805319-151805326 chr1:151805318-151805327
33	EP300	chr1:151804990-151805490	HepG2	liver:	n/a	chr1:151805297-151805310
34	CHD2	chr1:151805035-151805452	Hela-S3	cervix:	n/a	n/a
35	MXI1	chr1:151804864-151805655	SK-N-SH	brain:	n/a	n/a
36	MAX	chr1:151804936-151805499	HepG2	liver:	n/a	chr1:151805317-151805328 chr1:151805319-151805326 chr1:151805318-151805327
37	CEBPB	chr1:151804840-151805521	MCF-7	breast:	n/a	n/a
38	HEY1	chr1:151804884-151805613	HepG2	liver:	n/a	n/a
39	FOXA1	chr1:151804987-151805436	HepG2	liver:	n/a	n/a
40	MAZ	chr1:151804984-151805505	Hela-S3	cervix:	n/a	chr1:151805317-151805328 chr1:151805319-151805326 chr1:151805318-151805327
41	HCFC1	chr1:151802407-151805731	Hela-S3	cervix:	n/a	n/a
42	EP300	chr1:151804993-151805510	T-47D	breast:	n/a	chr1:151805297-151805310
43	SMC3	chr1:151804987-151805452	Hela-S3	cervix:	n/a	chr1:151805307-151805317
44	MAX	chr1:151804954-151805592	ECC-1	luminal epithelium:	n/a	chr1:151805317-151805328 chr1:151805319-151805326 chr1:151805318-151805327
45	HEY1	chr1:151805022-151805433	HepG2	liver:	n/a	n/a
46	MAX	chr1:151804657-151805797	MCF-7	breast:	n/a	chr1:151805317-151805328 chr1:151805319-151805326 chr1:151805318-151805327
47	GATA3	chr1:151804657-151805738	MCF-7	breast:	n/a	n/a
48	POLR2A	chr1:151805044-151805393	Hela-S3	cervix:	n/a	n/a
49	MYC	chr1:151805031-151805535	Hela-S3	cervix:	n/a	chr1:151805317-151805328 chr1:151805319-151805326 chr1:151805318-151805327
50	BHLHE40	chr1:151804786-151805661	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:151762059..151766604-chr1:151800169..151809078,15	MCF-7	breast:
2	chr1:151760926..151765128-chr1:151802888..151806720,6	MCF-7	breast:
3	chr1:151512695..151514361-chr1:151804056..151806637,3	MCF-7	breast:
4	chr1:151804439..151806613-chr1:152006311..152009166,3	MCF-7	breast:
5	chr1:151735081..151737738-chr1:151803314..151806226,2	MCF-7	breast:
6	chr1:151510723..151515515-chr1:151802413..151805096,5	MCF-7	breast:
7	chr1:151519770..151522144-chr1:151805041..151806645,2	MCF-7	breast:
8	chr1:151483209..151487051-chr1:151804533..151808098,3	MCF-7	breast:
9	chr1:151731676..151737592-chr1:151803957..151806544,6	MCF-7	breast:
10	chr1:151803084..151806304-chr1:151962981..151966430,4	MCF-7	breast:
11	chr1:151804012..151806616-chr1:151810661..151813276,2	K562	blood:
12	chr1:151804539..151806807-chr1:151808292..151812161,4	K562	blood:

Variant related genes	Relation type
RORC	TF binding region
ENSG00000232536	Chromatin interaction
ENSG00000182134	Chromatin interaction
ENSG00000143436	Chromatin interaction
ENSG00000143450	Chromatin interaction
ENSG00000225556	Chromatin interaction
ENSG00000143367	Chromatin interaction
ENSG00000197747	Chromatin interaction
ENSG00000143375	Chromatin interaction
ENSG00000203288	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11582525	0.90[CEU][hapmap];0.91[EUR][1000 genomes]
rs12126984	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3811417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811419	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4845602	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4845606	1.00[CEU][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.89[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72692781	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72692783	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7540799	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv516369	chr1:151780177-151820324	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv1804657	chr1:151784152-151825756	Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv1008033	chr1:151785029-151843154	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3811418	S100A16	cis	cerebellum	SCAN
rs3811418	PSMD4	cis	parietal	SCAN
rs3811418	C1orf51	cis	parietal	SCAN
rs3811418	SCNM1	cis	parietal	SCAN
rs3811418	S100A10	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151798400-151807000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr1:151799000-151807800	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr1:151800000-151806400	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr1:151801200-151807400	Enhancers	Primary T cells from cord blood	blood
5	chr1:151801200-151808000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:151801800-151805200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:151802000-151809400	Enhancers	Fetal Thymus	thymus
8	chr1:151802200-151805200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:151802200-151807000	Enhancers	Thymus	Thymus
10	chr1:151802400-151805800	Flanking Active TSS	Hela-S3	cervix
11	chr1:151802400-151808000	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr1:151802400-151810400	Weak transcription	Right Atrium	heart
13	chr1:151802600-151805400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr1:151802800-151811000	Enhancers	Placenta	Placenta
15	chr1:151803200-151805200	Weak transcription	Fetal Brain Male	brain
16	chr1:151803200-151805800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr1:151803400-151805400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:151803400-151805600	Enhancers	Adipose Nuclei	Adipose
19	chr1:151803400-151807000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:151803600-151806000	Weak transcription	Primary B cells from cord blood	blood
21	chr1:151803600-151806200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:151803800-151805200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr1:151803800-151805800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:151803800-151806000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr1:151803800-151808800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr1:151803800-151808800	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr1:151803800-151808800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr1:151803800-151808800	Weak transcription	A549	lung
29	chr1:151804000-151805200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr1:151804000-151805200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:151804000-151805800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr1:151804000-151806000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:151804000-151806200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr1:151804200-151805200	Weak transcription	Brain Germinal Matrix	brain
35	chr1:151804200-151805200	Enhancers	Fetal Intestine Small	intestine
36	chr1:151804200-151805800	Flanking Active TSS	HepG2	liver
37	chr1:151804200-151807200	Enhancers	Fetal Intestine Large	intestine
38	chr1:151804200-151808800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr1:151804400-151805200	Enhancers	Fetal Muscle Trunk	muscle
40	chr1:151804400-151805200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr1:151804400-151805200	Weak transcription	Dnd41	blood
42	chr1:151804400-151805600	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr1:151804400-151805600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
44	chr1:151804400-151805600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr1:151804400-151806000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:151804400-151806000	Enhancers	Esophagus	oesophagus
47	chr1:151804400-151806400	Enhancers	Fetal Muscle Leg	muscle
48	chr1:151804400-151807200	Flanking Active TSS	Liver	Liver
49	chr1:151804400-151809200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr1:151804400-151810200	Weak transcription	Gastric	stomach

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