Variant report

Variant	rs6683396
Chromosome Location	chr1:151171811-151171812
allele	C/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	YY1	chr1:151170657-151171852	GM12878	blood:	n/a	chr1:151171348-151171357 chr1:151171464-151171481
2	POLR2A	chr1:151170632-151171821	GM12892	blood:	n/a	n/a
3	MTA3	chr1:151170182-151171937	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:151170553-151171816	PANC-1	pancreas:	n/a	n/a
5	TCF7L2	chr1:151170777-151171887	HCT-116	colon:	n/a	chr1:151171516-151171530
6	POLR2A	chr1:151170497-151171813	PFSK-1	brain:	n/a	n/a
7	FOXM1	chr1:151170574-151171869	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:151170518-151172240	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:151170229-151171841	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr1:151170226-151171953	Hela-S3	cervix:	n/a	n/a
11	STAT5A	chr1:151170358-151171842	GM12878	blood:	n/a	chr1:151171350-151171362 chr1:151171363-151171387 chr1:151170754-151170762
12	POLR2A	chr1:151170218-151171838	HepG2	liver:	n/a	n/a
13	TCF12	chr1:151170318-151171891	A549	lung:	n/a	chr1:151171278-151171286
14	SIN3AK20	chr1:151170040-151171936	MCF-7	breast:	n/a	n/a
15	POLR2A	chr1:151170443-151172086	PFSK-1	brain:	n/a	n/a
16	YY1	chr1:151171225-151171828	ECC-1	luminal epithelium:	n/a	chr1:151171348-151171357 chr1:151171464-151171481
17	TCF12	chr1:151170552-151171814	ECC-1	luminal epithelium:	n/a	chr1:151171278-151171286
18	RUNX3	chr1:151170556-151172487	GM12878	blood:	n/a	n/a
19	POLR2A	chr1:151170525-151172237	GM12892	blood:	n/a	n/a
20	YY1	chr1:151170771-151171937	GM12892	blood:	n/a	chr1:151171348-151171357 chr1:151171464-151171481
21	MAX	chr1:151169994-151171941	MCF-7	breast:	n/a	chr1:151171346-151171356 chr1:151170927-151170936
22	CEBPB	chr1:151171783-151171812	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr1:151170519-151171832	ProgFib	skin:	n/a	n/a
24	POLR2A	chr1:151170513-151171825	U87	brain:	n/a	n/a
25	REST	chr1:151170463-151172040	H1-neurons	neurons:	n/a	n/a
26	POU2F2	chr1:151170765-151172075	GM12891	blood:	n/a	chr1:151171446-151171458 chr1:151171345-151171357
27	HDAC2	chr1:151169975-151171995	MCF-7	breast:	n/a	chr1:151170877-151170886
28	PML	chr1:151170284-151171849	GM12878	blood:	n/a	n/a
29	POLR2A	chr1:151170450-151171991	SK-N-MC	brain:	n/a	n/a
30	POLR2A	chr1:151170651-151171863	K562	blood:	n/a	n/a
31	POLR2A	chr1:151170554-151171937	H1-hESC	embryonic stem cell:	n/a	n/a
32	RUNX3	chr1:151170608-151172335	GM12878	blood:	n/a	n/a
33	RCOR1	chr1:151170169-151171853	Hela-S3	cervix:	n/a	n/a
34	MAX	chr1:151170226-151171913	A549	lung:	n/a	chr1:151171346-151171356 chr1:151170927-151170936
35	NRF1	chr1:151170124-151171978	SK-N-SH	brain:	n/a	chr1:151171009-151171020 chr1:151171009-151171020 chr1:151171348-151171357 chr1:151171006-151171020 chr1:151171009-151171023 chr1:151171009-151171018 chr1:151171011-151171020 chr1:151170876-151170885
36	TAF1	chr1:151170612-151171904	ECC-1	luminal epithelium:	n/a	n/a
37	POLR2A	chr1:151170619-151171958	GM12892	blood:	n/a	n/a
38	POLR2A	chr1:151170563-151171854	HCT-116	colon:	n/a	n/a
39	SMARCB1	chr1:151170677-151171883	Hela-S3	cervix:	n/a	n/a
40	TBP	chr1:151170270-151171818	Hela-S3	cervix:	n/a	n/a
41	YY1	chr1:151170663-151171897	A549	lung:	n/a	chr1:151171348-151171357 chr1:151171464-151171481
42	YY1	chr1:151170714-151172070	GM12878	blood:	n/a	chr1:151171348-151171357 chr1:151171464-151171481
43	ZNF263	chr1:151170478-151171922	HEK293-T-REx	kidney:	n/a	chr1:151171593-151171614
44	YY1	chr1:151170727-151171918	GM12891	blood:	n/a	chr1:151171348-151171357 chr1:151171464-151171481
45	POLR2A	chr1:151170736-151172131	IMR90	lung:	n/a	n/a
46	MAX	chr1:151169944-151171900	MCF-7	breast:	n/a	chr1:151171346-151171356 chr1:151170927-151170936
47	HA-E2F1	chr1:151169528-151171929	MCF-7	breast:	n/a	chr1:151171348-151171360 chr1:151170424-151170436 chr1:151171010-151171019 chr1:151171669-151171684 chr1:151171348-151171357
48	POLR2A	chr1:151171711-151171868	GM12878	blood:	n/a	n/a
49	POLR2A	chr1:151170670-151171898	H1-hESC	embryonic stem cell:	n/a	n/a
50	TCF7L2	chr1:151171316-151171811	Hela-S3	cervix:	n/a	chr1:151171516-151171530

No.	Distal block	Cell Line	Cell type
1	1:151171193-151178589..1:151411623-151426875	GM12878	blood:
2	chr1:151171270..151173891-chr1:151252685..151255060,3	K562	blood:
3	1:151171193-151178589..1:151246650-151254384	GM12878	blood:
4	chr1:151170179..151172284-chr1:151482238..151485195,2	MCF-7	breast:
5	chr1:151169497..151174843-chr1:151224312..151231181,18	MCF-7	breast:
6	chr1:151171256..151175527-chr1:151178181..151182275,7	MCF-7	breast:
7	chr1:151162057..151164706-chr1:151165181..151172008,8	K562	blood:
8	1:151171193-151178589..1:151333184-151350267	GM12878	blood:
9	1:151171193-151178589..1:151219411-151234038	GM12878	blood:
10	chr1:151171485..151173202-chr17:57182944..57185192,2	MCF-7	breast:
11	1:151171193-151178589..1:151254384-151268403	Hela-S3	cervix:
12	chr1:151166432..151169145-chr1:151169439..151172527,5	MCF-7	breast:
13	1:151171193-151178589..1:151516085-151535167	GM12878	blood:
14	chr1:151170967..151173717-chr1:151426450..151428273,2	MCF-7	breast:
15	chr1:151165541..151174157-chr1:151252015..151257857,16	MCF-7	breast:
16	chr1:150979099..150980863-chr1:151170963..151172486,2	MCF-7	breast:
17	1:151171193-151178589..1:151203965-151215310	GM12878	blood:
18	chr1:151156826..151164982-chr1:151165389..151172985,25	MCF-7	breast:
19	chr1:151136716..151140911-chr1:151168778..151172657,5	MCF-7	breast:
20	1:151171193-151178589..1:151368336-151375897	Hela-S3	cervix:
21	chr1:151171136..151172895-chr1:151252862..151254583,2	K562	blood:
22	chr1:151168724..151174586-chr1:151252405..151256834,10	MCF-7	breast:
23	chr1:151170674..151172337-chr8:125550185..125552873,2	MCF-7	breast:
24	chr1:151170127..151171898-chr10:95720093..95723081,2	MCF-7	breast:
25	chr1:151171114..151172618-chr15:89662367..89664545,2	MCF-7	breast:
26	chr1:151136857..151140256-chr1:151168802..151172321,4	MCF-7	breast:
27	1:151171193-151178589..1:151496437-151509688	Hela-S3	cervix:
28	chr1:151170887..151173171-chr1:151225503..151227858,2	K562	blood:
29	chr1:151147180..151151121-chr1:151169846..151172495,3	MCF-7	breast:
30	1:151171193-151178589..1:151270864-151283078	K562	blood:
31	1:151171193-151178589..1:151618750-151636526	Hela-S3	cervix:
32	chr1:151169931..151174343-chr1:151224824..151227591,5	MCF-7	breast:
33	chr1:151169798..151173171-chr1:151225503..151227858,3	K562	blood:
34	1:151171193-151178589..1:151309061-151322694	Hela-S3	cervix:

Variant related genes	Relation type
VPS72	TF binding region
ENSG00000223861	Chromatin interaction
ENSG00000159377	Chromatin interaction
ENSG00000143442	Chromatin interaction
ENSG00000265753	Chromatin interaction
ENSG00000143373	Chromatin interaction
ENSG00000163155	Chromatin interaction
ENSG00000237976	Chromatin interaction
ENSG00000207606	Chromatin interaction
ENSG00000143375	Chromatin interaction
ENSG00000143390	Chromatin interaction
ENSG00000159352	Chromatin interaction
ENSG00000224645	Chromatin interaction
ENSG00000143409	Chromatin interaction
ENSG00000239151	Chromatin interaction
ENSG00000224738	Chromatin interaction
ENSG00000143376	Chromatin interaction
ENSG00000232671	Chromatin interaction
ENSG00000163157	Chromatin interaction
ENSG00000143398	Chromatin interaction
ENSG00000163159	Chromatin interaction
ENSG00000163156	Chromatin interaction
ENSG00000180764	Chromatin interaction
ENSG00000147684	Chromatin interaction
ENSG00000108395	Chromatin interaction
ENSG00000252840	Chromatin interaction
ENSG00000143393	Chromatin interaction
ENSG00000143367	Chromatin interaction
ENSG00000143416	Chromatin interaction
ENSG00000147687	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10749660	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10888406	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10888408	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11204785	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11204791	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11807075	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12022732	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12040384	0.83[ASN][1000 genomes]
rs12048670	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12062719	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12080778	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12407426	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16827941	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16833079	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1892196	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2275900	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41302131	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4291501	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4520422	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4970944	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4971013	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4971015	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4971016	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4971021	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4971023	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4971025	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4971026	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58323986	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61817972	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6587559	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6587562	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6681071	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6681163	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6686402	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6695344	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6701325	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7521064	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7527032	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7532935	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7539584	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7544947	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151167000-151172000	Active TSS	Colonic Mucosa	Colon
2	chr1:151170000-151173000	Active TSS	Esophagus	oesophagus
3	chr1:151170200-151173200	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr1:151170200-151173200	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr1:151170200-151173200	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr1:151170200-151173200	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr1:151170200-151173200	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr1:151170200-151173200	Active TSS	Right Ventricle	heart
9	chr1:151170200-151173400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:151170200-151173600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:151170400-151172000	Active TSS	Fetal Muscle Trunk	muscle
12	chr1:151170400-151172800	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr1:151170400-151173000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:151170400-151173000	Active TSS	Psoas Muscle	Psoas
15	chr1:151170400-151173000	Active TSS	Right Atrium	heart
16	chr1:151170400-151173200	Active TSS	H1 Cell Line	embryonic stem cell
17	chr1:151170400-151173200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:151170400-151173200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:151170400-151173200	Active TSS	Aorta	Aorta
20	chr1:151170400-151173200	Active TSS	Ovary	ovary
21	chr1:151170600-151172000	Active TSS	Brain Angular Gyrus	brain
22	chr1:151170600-151172000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:151170600-151172000	Active TSS	Colon Smooth Muscle	Colon
24	chr1:151170600-151172000	Active TSS	Fetal Brain Male	brain
25	chr1:151170600-151172000	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr1:151170600-151172000	Active TSS	Rectal Mucosa Donor 31	rectum
27	chr1:151170600-151172000	Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr1:151170600-151172200	Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr1:151170600-151172200	Active TSS	Brain Anterior Caudate	brain
30	chr1:151170600-151172200	Active TSS	Brain Cingulate Gyrus	brain
31	chr1:151170600-151172200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
32	chr1:151170600-151172200	Active TSS	Fetal Brain Female	brain
33	chr1:151170600-151172200	Active TSS	Fetal Lung	lung
34	chr1:151170600-151172200	Active TSS	Pancreas	Pancrea
35	chr1:151170600-151172200	Active TSS	Sigmoid Colon	Sigmoid Colon
36	chr1:151170600-151172200	Active TSS	Stomach Smooth Muscle	stomach
37	chr1:151170600-151172200	Active TSS	Thymus	Thymus
38	chr1:151170600-151172400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:151170600-151172400	Active TSS	iPS-18 Cell Line	embryonic stem cell
40	chr1:151170600-151172400	Active TSS	Fetal Stomach	stomach
41	chr1:151170600-151172400	Active TSS	Rectal Smooth Muscle	rectum
42	chr1:151170600-151172600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr1:151170600-151172600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:151170600-151172600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:151170600-151172600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr1:151170600-151172800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:151170600-151172800	Bivalent/Poised TSS	HepG2	liver
48	chr1:151170600-151173000	Active TSS	HUES6 Cell Line	embryonic stem cell
49	chr1:151170600-151173000	Active TSS	Fetal Intestine Large	intestine
50	chr1:151170600-151173200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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