Variant report

Variant	rs3183927
Chromosome Location	chr9:100684757-100684758
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	CTCF	chr9:100684584-100684822	HUVEC	blood vessel:	n/a	n/a
2	JUN	chr9:100684224-100684810	K562	blood:	n/a	chr9:100684512-100684521 chr9:100684511-100684524
3	MYC	chr9:100684236-100686457	K562	blood:	n/a	chr9:100684539-100684548 chr9:100684537-100684550 chr9:100684535-100684550 chr9:100684555-100684564 chr9:100684539-100684548 chr9:100684550-100684569 chr9:100684534-100684553 chr9:100684539-100684549 chr9:100684554-100684565 chr9:100684537-100684550 chr9:100684537-100684550 chr9:100684540-100684549
4	NFIC	chr9:100684232-100685034	HepG2	liver:	n/a	n/a
5	JUN	chr9:100684226-100684967	K562	blood:	n/a	chr9:100684512-100684521 chr9:100684511-100684524
6	EBF1	chr9:100684333-100684909	GM12878	blood:	n/a	n/a
7	CREB1	chr9:100684299-100684977	A549	lung:	n/a	chr9:100684510-100684523
8	CTCF	chr9:100684586-100684861	GM13976	blood:	n/a	n/a
9	CTCF	chr9:100684640-100684790	HEK293	kidney:	n/a	n/a
10	CTCF	chr9:100684660-100684810	AG09309	skin:	n/a	n/a
11	CTCF	chr9:100684620-100684770	AG10803	skin:	n/a	n/a
12	CTCF	chr9:100684620-100684770	HCPEpiC	choroid plexus:	n/a	n/a
13	CTCF	chr9:100684640-100684790	AG04449	skin:	n/a	n/a
14	MAX	chr9:100684180-100685291	A549	lung:	n/a	chr9:100684539-100684548 chr9:100684537-100684550 chr9:100684535-100684550 chr9:100684555-100684564 chr9:100684539-100684548 chr9:100684550-100684569 chr9:100684534-100684553 chr9:100684539-100684549 chr9:100684554-100684565 chr9:100684537-100684550 chr9:100684537-100684550 chr9:100684540-100684549
15	SPI1	chr9:100684651-100684982	K562	blood:	n/a	n/a
16	JUND	chr9:100684273-100684764	H1-hESC	embryonic stem cell:	n/a	chr9:100684512-100684521
17	CTCF	chr9:100684640-100684790	Caco-2	colon:	n/a	n/a
18	YY1	chr9:100684333-100685148	ECC-1	luminal epithelium:	n/a	n/a
19	CREB1	chr9:100684305-100685107	A549	lung:	n/a	chr9:100684510-100684523
20	CTCF	chr9:100684517-100684884	MCF-7	breast:	n/a	n/a
21	MYC	chr9:100684391-100684979	MCF-7	breast:	n/a	chr9:100684539-100684548 chr9:100684537-100684550 chr9:100684535-100684550 chr9:100684555-100684564 chr9:100684539-100684548 chr9:100684550-100684569 chr9:100684534-100684553 chr9:100684539-100684549 chr9:100684554-100684565 chr9:100684537-100684550 chr9:100684537-100684550 chr9:100684540-100684549
22	SIN3AK20	chr9:100684188-100685243	A549	lung:	n/a	n/a
23	YY1	chr9:100684227-100685064	GM12878	blood:	n/a	n/a
24	E2F6	chr9:100684405-100685231	A549	lung:	n/a	chr9:100684840-100684849 chr9:100684511-100684520 chr9:100684513-100684522
25	TAF1	chr9:100684157-100685060	K562	blood:	n/a	n/a
26	CTCF	chr9:100684680-100684830	HPAF	blood vessel:	n/a	n/a
27	MTA3	chr9:100684069-100685757	GM12878	blood:	n/a	n/a
28	JUND	chr9:100684107-100685197	K562	blood:	n/a	chr9:100684512-100684521
29	RAD21	chr9:100684343-100684895	HepG2	liver:	n/a	n/a
30	SIN3AK20	chr9:100684218-100685070	A549	lung:	n/a	n/a
31	POLR2A	chr9:100684079-100685266	ProgFib	skin:	n/a	n/a
32	CTCF	chr9:100684620-100684770	HBMEC	blood vessel:	n/a	n/a
33	POU2F2	chr9:100684212-100685102	GM12891	blood:	n/a	n/a
34	GABPA	chr9:100684261-100685147	MCF-7	breast:	n/a	chr9:100684839-100684850 chr9:100684496-100684503 chr9:100684839-100684853 chr9:100684816-100684823 chr9:100684841-100684850
35	POLR2A	chr9:100684075-100685243	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr9:100684086-100685180	HUVEC	blood vessel:	n/a	n/a
37	SIX5	chr9:100684244-100684889	A549	lung:	n/a	chr9:100684283-100684297
38	MAX	chr9:100684208-100685370	K562	blood:	n/a	chr9:100684555-100684564 chr9:100684537-100684550 chr9:100684539-100684549 chr9:100684537-100684550 chr9:100684534-100684553 chr9:100684540-100684549 chr9:100684535-100684550 chr9:100684539-100684548 chr9:100684539-100684548 chr9:100684550-100684569 chr9:100684554-100684565 chr9:100684537-100684550
39	REST	chr9:100684287-100684826	SK-N-SH	brain:	n/a	n/a
40	TCF12	chr9:100684179-100685245	ECC-1	luminal epithelium:	n/a	n/a
41	POU2F2	chr9:100684232-100685014	GM12878	blood:	n/a	n/a
42	SPI1	chr9:100684668-100684961	K562	blood:	n/a	n/a
43	SIN3AK20	chr9:100684267-100685018	PANC-1	pancreas:	n/a	n/a
44	CHD2	chr9:100684330-100685071	H1-hESC	embryonic stem cell:	n/a	n/a
45	CTCF	chr9:100684559-100684838	Hela-S3	cervix:	n/a	n/a
46	REST	chr9:100683900-100685385	H1-neurons	neurons:	n/a	n/a
47	HEY1	chr9:100684208-100685067	HepG2	liver:	n/a	chr9:100684511-100684520 chr9:100684513-100684522
48	RUNX3	chr9:100684225-100685162	GM12878	blood:	n/a	n/a
49	STAT3	chr9:100684265-100684873	GM12878	blood:	n/a	n/a
50	POLR2A	chr9:100683994-100685241	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:52710261..52711062-chr9:100684451..100685047,2	Hela-S3	cervix:
2	chr9:100682029..100688801-chr9:100740969..100749393,29	MCF-7	breast:
3	chr9:100682922..100687440-chr9:100817123..100820939,8	MCF-7	breast:
4	chr2:73612640..73613510-chr9:100684147..100685046,2	Hela-S3	cervix:
5	chr9:100684436..100684977-chrX:40440205..40441030,2	Hela-S3	cervix:
6	chr2:201981489..201982019-chr9:100684640..100685215,2	Hela-S3	cervix:
7	chr19:5690248..5690846-chr9:100684329..100685317,2	Hela-S3	cervix:
8	chr9:100684661..100686943-chr9:100794140..100799259,5	K562	blood:
9	chr9:100683922..100686421-chr9:100749688..100751954,2	MCF-7	breast:
10	chr9:100393929..100396893-chr9:100683273..100687162,3	K562	blood:
11	chr9:100684640..100686948-chr9:100880759..100882563,2	K562	blood:
12	chr9:100458137..100459680-chr9:100684005..100686050,2	MCF-7	breast:
13	chr9:100683337..100688322-chr9:101015638..101019207,5	MCF-7	breast:
14	chr9:100683217..100685598-chr9:100817702..100819594,2	MCF-7	breast:
15	chr9:100678422..100708679-chr9:100734559..100755577,174	K562	blood:
16	chr9:100683356..100686345-chr9:100832359..100837233,6	MCF-7	breast:
17	chr9:100683172..100685162-chr9:100749919..100752438,2	MCF-7	breast:
18	chr9:100683079..100687048-chr9:101015405..101020638,4	K562	blood:
19	chr19:55895131..55895969-chr9:100684595..100685317,2	Hela-S3	cervix:
20	chr9:100683358..100685652-chr9:101557664..101560368,2	K562	blood:
21	chr9:100682507..100691249-chr9:100739828..100748095,35	MCF-7	breast:
22	chr2:162016997..162017961-chr9:100684374..100684996,2	Hela-S3	cervix:
23	chr17:7387588..7388177-chr9:100684359..100685331,2	Hela-S3	cervix:
24	chr1:43637450..43638367-chr9:100684269..100684815,2	Hela-S3	cervix:
25	chr2:38977694..38978560-chr9:100684515..100685296,2	HCT-116	colon:
26	chr9:100684278..100686693-chr9:100816052..100820620,8	K562	blood:
27	chr7:138145133..138145677-chr9:100684432..100685419,2	Hela-S3	cervix:
28	chr6:133561719..133562540-chr9:100684595..100685146,2	Hela-S3	cervix:
29	chr20:48599018..48599575-chr9:100684497..100685019,2	Hela-S3	cervix:
30	chr10:35484287..35485259-chr9:100684125..100684996,2	Hela-S3	cervix:
31	chr2:204400007..204400680-chr9:100684347..100685133,2	Hela-S3	cervix:
32	chr9:100679913..100686278-chr9:100816188..100820459,11	K562	blood:
33	chr17:52978107..52978650-chr9:100684226..100685178,2	Hela-S3	cervix:
34	chr9:19048684..19049542-chr9:100684339..100685327,2	Hela-S3	cervix:
35	chr6:31703444..31704424-chr9:100684339..100685051,2	Hela-S3	cervix:
36	chr9:100675954..100709047-chr9:100737887..100755543,175	K562	blood:
37	chr16:10674320..10675054-chr9:100684357..100685157,2	Hela-S3	cervix:
38	chr1:145382412..145382912-chr9:100684586..100685344,2	Hela-S3	cervix:
39	chr9:100683227..100687367-chr9:100758311..100762778,5	K562	blood:

Variant related genes	Relation type
C9orf156	TF binding region
ENSG00000136925	Chromatin interaction
ENSG00000095794	Chromatin interaction
ENSG00000233493	Chromatin interaction
ENSG00000095383	Chromatin interaction
ENSG00000122779	Chromatin interaction
ENSG00000136937	Chromatin interaction
ENSG00000173166	Chromatin interaction
ENSG00000233396	Chromatin interaction
ENSG00000181222	Chromatin interaction
ENSG00000124216	Chromatin interaction
ENSG00000109184	Chromatin interaction
ENSG00000243710	Chromatin interaction
ENSG00000201558	Chromatin interaction
ENSG00000165138	Chromatin interaction
ENSG00000141198	Chromatin interaction
ENSG00000106785	Chromatin interaction
ENSG00000112319	Chromatin interaction
ENSG00000236896	Chromatin interaction
ENSG00000136936	Chromatin interaction
ENSG00000136938	Chromatin interaction
ENSG00000116127	Chromatin interaction
ENSG00000212521	Chromatin interaction
ENSG00000213853	Chromatin interaction
ENSG00000155876	Chromatin interaction
ENSG00000182220	Chromatin interaction
ENSG00000117395	Chromatin interaction
ENSG00000130255	Chromatin interaction
ENSG00000136560	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000213719	Chromatin interaction
ENSG00000095380	Chromatin interaction
ENSG00000003402	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10119795	0.81[CHB][hapmap]
rs10760021	0.93[CHB][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10760022	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10984361	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10984373	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10984405	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10984466	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10984499	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10984506	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12237296	0.86[JPT][hapmap]
rs12238579	0.81[CHB][hapmap]
rs12377604	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1475695	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1475696	1.00[CEU][hapmap];0.97[GIH][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1561958	0.81[CHB][hapmap]
rs17431614	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17431934	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2120263	0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[LWK][hapmap];0.84[MKK][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2282192	0.94[CHB][hapmap];1.00[CHD][hapmap];0.96[LWK][hapmap];0.82[MKK][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2417577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3183928	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3758253	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3758254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3780420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3808894	0.91[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3824496	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4631576	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.90[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4743145	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4743147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55737216	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6586	0.81[CHB][hapmap]
rs66990486	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7030887	1.00[CEU][hapmap];0.97[GIH][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7030907	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs755109	1.00[CEU][hapmap];0.97[GIH][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7861658	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7864655	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893611	chr9:100561055-100739888	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1048135	chr9:100666931-100717030	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	nsv525113	chr9:100669799-100686815	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv524282	chr9:100677166-100684757	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3183927	C9orf156	cis	Esophagus Muscularis	GTEx
rs3183927	WNK2	cis	parietal	SCAN
rs3183927	C9orf156	cis	cerebellum	SCAN
rs3183927	TMOD1	cis	parietal	SCAN
rs3183927	NANS	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100683000-100685400	Active TSS	K562	blood
2	chr9:100683000-100685600	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr9:100683400-100685400	Active TSS	Primary T cells from cord blood	blood
4	chr9:100683400-100685400	Active TSS	Duodenum Mucosa	Duodenum
5	chr9:100683400-100685400	Active TSS	GM12878-XiMat	blood
6	chr9:100683400-100685600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr9:100683600-100685200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr9:100683600-100685400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr9:100683600-100685400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
10	chr9:100683600-100685400	Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr9:100683600-100686400	Active TSS	Thymus	Thymus
12	chr9:100683800-100685000	Active TSS	Hela-S3	cervix
13	chr9:100683800-100685400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
14	chr9:100683800-100685400	Active TSS	HSMM	muscle
15	chr9:100683800-100685800	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr9:100683800-100686200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr9:100683800-100686200	Active TSS	Fetal Brain Female	brain
18	chr9:100683800-100686200	Active TSS	Rectal Smooth Muscle	rectum
19	chr9:100684000-100685000	Active TSS	HSMMtube	muscle
20	chr9:100684000-100685200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
21	chr9:100684000-100685400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr9:100684000-100685400	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr9:100684000-100685400	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr9:100684000-100685400	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr9:100684000-100685400	Active TSS	Brain Cingulate Gyrus	brain
26	chr9:100684000-100685400	Active TSS	Brain Hippocampus Middle	brain
27	chr9:100684000-100685400	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr9:100684000-100685400	Active TSS	Fetal Intestine Small	intestine
29	chr9:100684000-100685400	Active TSS	Fetal Kidney	kidney
30	chr9:100684000-100685400	Active TSS	Fetal Stomach	stomach
31	chr9:100684000-100685400	Active TSS	Psoas Muscle	Psoas
32	chr9:100684000-100685400	Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr9:100684000-100685400	Active TSS	A549	lung
34	chr9:100684000-100685400	Active TSS	HMEC	breast
35	chr9:100684000-100685400	Active TSS	NH-A	brain
36	chr9:100684000-100685400	Active TSS	NHDF-Ad	bronchial
37	chr9:100684000-100685600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr9:100684000-100685600	Active TSS	Colon Smooth Muscle	Colon
39	chr9:100684000-100685800	Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr9:100684000-100686000	Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr9:100684000-100686000	Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr9:100684000-100686000	Active TSS	Aorta	Aorta
43	chr9:100684000-100686000	Active TSS	Colonic Mucosa	Colon
44	chr9:100684000-100686000	Flanking Active TSS	Placenta	Placenta
45	chr9:100684000-100686200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr9:100684000-100686200	Active TSS	Brain Substantia Nigra	brain
47	chr9:100684000-100686200	Active TSS	Fetal Intestine Large	intestine
48	chr9:100684000-100686200	Active TSS	Right Atrium	heart
49	chr9:100684000-100686200	Active TSS	Right Ventricle	heart
50	chr9:100684000-100686400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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