Variant report

Variant	rs12084911
Chromosome Location	chr1:174128404-174128405
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	GTF2B	chr1:174128283-174128805	K562	blood:	n/a	n/a
2	BHLHE40	chr1:174127962-174129636	K562	blood:	n/a	chr1:174128488-174128504
3	MAX	chr1:174128012-174128923	GM12878	blood:	n/a	n/a
4	MAX	chr1:174128221-174129324	K562	blood:	n/a	n/a
5	JUND	chr1:174127997-174128905	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr1:174127564-174130052	Raji	blood:	n/a	n/a
7	NR2F2	chr1:174127922-174129594	K562	blood:	n/a	n/a
8	E2F6	chr1:174128017-174129102	A549	lung:	n/a	chr1:174128487-174128497 chr1:174129032-174129041 chr1:174128376-174128387
9	ATF1	chr1:174127630-174128539	K562	blood:	n/a	n/a
10	RCOR1	chr1:174128094-174128862	GM12878	blood:	n/a	n/a
11	E2F4	chr1:174128148-174129668	K562	blood:	n/a	chr1:174128487-174128497 chr1:174129032-174129041 chr1:174128385-174128396
12	TBL1XR1	chr1:174127569-174128829	K562	blood:	n/a	n/a
13	E2F1	chr1:174128168-174129464	Hela-S3	cervix:	n/a	chr1:174128487-174128497 chr1:174129032-174129041
14	TAF1	chr1:174128205-174128841	HepG2	liver:	n/a	n/a
15	POLR2A	chr1:174128044-174129014	ECC-1	luminal epithelium:	n/a	n/a
16	POLR2A	chr1:174128218-174129319	H1-neurons	neurons:	n/a	n/a
17	SREBP1	chr1:174125904-174128766	GM12878	blood:	n/a	n/a
18	EGR1	chr1:174128014-174129318	HCT-116	colon:	n/a	chr1:174128529-174128538 chr1:174129031-174129041 chr1:174128484-174128498 chr1:174128953-174128966
19	POLR2A	chr1:174127563-174129733	GM12878	blood:	n/a	n/a
20	NRF1	chr1:174128261-174128626	GM12878	blood:	n/a	chr1:174128445-174128456 chr1:174128476-174128487
21	MTA3	chr1:174127321-174128503	GM12878	blood:	n/a	n/a
22	NRF1	chr1:174128010-174128975	SK-N-SH	brain:	n/a	chr1:174128445-174128456 chr1:174128476-174128487
23	SMC3	chr1:174128188-174129645	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr1:174127613-174129697	GM15510	blood:	n/a	n/a
25	E2F6	chr1:174128195-174129230	H1-hESC	embryonic stem cell:	n/a	chr1:174128487-174128497 chr1:174129032-174129041 chr1:174128376-174128387
26	CTBP2	chr1:174128325-174129672	H1-hESC	embryonic stem cell:	n/a	n/a
27	SIN3AK20	chr1:174127618-174129756	MCF-7	breast:	n/a	n/a
28	POLR2A	chr1:174127680-174129746	PBDE	blood:	n/a	n/a
29	RELA	chr1:174127667-174129632	GM10847	blood:	n/a	chr1:174129361-174129370 chr1:174129361-174129370
30	ZNF143	chr1:174128257-174129571	Hela-S3	cervix:	n/a	chr1:174128491-174128501 chr1:174128771-174128781 chr1:174129409-174129427
31	RELA	chr1:174127358-174129544	GM19193	blood:	n/a	chr1:174129361-174129370 chr1:174129361-174129370
32	ETS1	chr1:174128230-174129632	K562	blood:	n/a	chr1:174128756-174128763 chr1:174129030-174129041 chr1:174128486-174128497 chr1:174128489-174128500
33	IRF1	chr1:174127960-174128920	K562	blood:	n/a	n/a
34	TAF7	chr1:174128202-174128927	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr1:174128230-174129757	HepG2	liver:	n/a	n/a
36	RELA	chr1:174126135-174129608	GM18505	blood:	n/a	chr1:174129361-174129370 chr1:174129361-174129370
37	POLR2A	chr1:174128141-174128874	HUVEC	blood vessel:	n/a	n/a
38	TBP	chr1:174128195-174128830	HepG2	liver:	n/a	n/a
39	CHD2	chr1:174128393-174128780	HepG2	liver:	n/a	n/a
40	POLR2A	chr1:174128237-174129008	MCF-7	breast:	n/a	n/a
41	TAF1	chr1:174128259-174128843	GM12892	blood:	n/a	n/a
42	MEF2A	chr1:174128164-174129579	GM12878	blood:	n/a	n/a
43	POLR2A	chr1:174128115-174129623	Hela-S3	cervix:	n/a	n/a
44	YY1	chr1:174128316-174128713	SK-N-SH_RA	brain:	n/a	chr1:174128486-174128497 chr1:174128487-174128501 chr1:174128486-174128495 chr1:174128489-174128498
45	POLR2A	chr1:174127833-174129498	HepG2	liver:	n/a	n/a
46	SIN3AK20	chr1:174128200-174129646	PANC-1	pancreas:	n/a	n/a
47	POLR2A	chr1:174128141-174129845	MCF10A-Er-Src	breast:	n/a	n/a
48	POLR2A	chr1:174128027-174129139	SK-N-MC	brain:	n/a	n/a
49	SIN3A	chr1:174127905-174129648	H1-hESC	embryonic stem cell:	n/a	chr1:174128772-174128781
50	RAD21	chr1:174128255-174128766	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:173791511..173794568-chr1:174127376..174130126,4	K562	blood:
2	chr1:173990484..173993026-chr1:174127463..174130354,3	K562	blood:
3	chr1:149859137..149859656-chr1:174128361..174129122,2	Hela-S3	cervix:
4	chr1:173990191..173994093-chr1:174126470..174130234,3	MCF-7	breast:
5	chr1:174127938..174128894-chr2:24306476..24307311,2	Hela-S3	cervix:
6	chr1:174128312..174130705-chr1:174967510..174969928,2	K562	blood:
7	chr1:174128367..174129924-chr16:2014665..2017256,2	K562	blood:
8	chr1:173837020..173839325-chr1:174127377..174129524,4	K562	blood:
9	chr1:173835391..173837802-chr1:174127164..174130207,3	MCF-7	breast:
10	chr1:173836251..173838308-chr1:174127483..174129757,2	MCF-7	breast:
11	chr1:173991432..173994922-chr1:174124746..174129302,4	K562	blood:
12	chr1:174127972..174128721-chr3:57993847..57994573,2	Hela-S3	cervix:
13	chr1:174128038..174128892-chr9:139440176..139441167,2	Hela-S3	cervix:
14	chr1:173835729..173840438-chr1:174127915..174131019,7	K562	blood:
15	chr1:174128312..174129852-chr1:174967356..174969010,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RC3H1-1	chr1:174128302-174128425	ENSG00000227373
2	lnc-RC3H1-1	chr1:174128302-174128799	NONHSAT007722

Variant related genes	Relation type
ENSG00000227373	TF binding region
RABGAP1L	TF binding region
ENSG00000224977	Chromatin interaction
ENSG00000237886	Chromatin interaction
ENSG00000116161	Chromatin interaction
ENSG00000115129	Chromatin interaction
ENSG00000117593	Chromatin interaction
ENSG00000265181	Chromatin interaction
ENSG00000179580	Chromatin interaction
ENSG00000136068	Chromatin interaction
ENSG00000255198	Chromatin interaction
ENSG00000140988	Chromatin interaction
ENSG00000185278	Chromatin interaction
ENSG00000148400	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000120334	Chromatin interaction
ENSG00000234741	Chromatin interaction
ENSG00000135870	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10489257	1.00[EUR][1000 genomes]
rs10912700	1.00[EUR][1000 genomes]
rs10912701	1.00[EUR][1000 genomes]
rs10912707	1.00[EUR][1000 genomes]
rs10912708	1.00[EUR][1000 genomes]
rs10912711	1.00[EUR][1000 genomes]
rs10912712	1.00[EUR][1000 genomes]
rs10912725	1.00[EUR][1000 genomes]
rs10912742	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912743	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912744	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912748	1.00[EUR][1000 genomes]
rs10912760	1.00[EUR][1000 genomes]
rs10912767	1.00[EUR][1000 genomes]
rs10912768	1.00[EUR][1000 genomes]
rs12057220	1.00[EUR][1000 genomes]
rs12058498	1.00[EUR][1000 genomes]
rs12059636	1.00[EUR][1000 genomes]
rs12061013	1.00[EUR][1000 genomes]
rs12062801	1.00[EUR][1000 genomes]
rs12063273	1.00[EUR][1000 genomes]
rs12063296	1.00[EUR][1000 genomes]
rs12064818	1.00[EUR][1000 genomes]
rs12065194	1.00[EUR][1000 genomes]
rs12066028	1.00[EUR][1000 genomes]
rs12067109	1.00[EUR][1000 genomes]
rs12067191	1.00[EUR][1000 genomes]
rs12067445	1.00[EUR][1000 genomes]
rs12068440	1.00[EUR][1000 genomes]
rs12069446	1.00[EUR][1000 genomes]
rs12069450	1.00[EUR][1000 genomes]
rs12070328	1.00[EUR][1000 genomes]
rs12071243	1.00[EUR][1000 genomes]
rs12072553	1.00[EUR][1000 genomes]
rs12073448	1.00[EUR][1000 genomes]
rs12073453	1.00[EUR][1000 genomes]
rs12075085	1.00[EUR][1000 genomes]
rs12075263	1.00[EUR][1000 genomes]
rs12076425	1.00[EUR][1000 genomes]
rs12077462	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12078222	1.00[EUR][1000 genomes]
rs12078645	1.00[EUR][1000 genomes]
rs12078817	1.00[EUR][1000 genomes]
rs12079274	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12079650	1.00[EUR][1000 genomes]
rs12081444	1.00[EUR][1000 genomes]
rs12081595	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12082017	1.00[EUR][1000 genomes]
rs12092291	1.00[EUR][1000 genomes]
rs12094364	1.00[EUR][1000 genomes]
rs12096013	1.00[EUR][1000 genomes]
rs1322781	1.00[EUR][1000 genomes]
rs1467397	1.00[EUR][1000 genomes]
rs16846878	1.00[EUR][1000 genomes]
rs1956522	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6673147	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6682041	1.00[EUR][1000 genomes]
rs7550107	1.00[EUR][1000 genomes]
rs997165	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831937	chr1:173949373-174131463	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv465661	chr1:174014507-174152688	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv548193	chr1:174014507-174152688	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv872552	chr1:174061844-174469748	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv1008314	chr1:174080192-174311023	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv535207	chr1:174080192-174311023	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	esv1799250	chr1:174119038-174484277	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 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	chr1:174127600-174129200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr1:174127600-174129200	Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr1:174127600-174129400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr1:174127600-174129400	Active TSS	Fetal Stomach	stomach
5	chr1:174127600-174129600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:174127600-174129600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:174127600-174129600	Active TSS	Rectal Smooth Muscle	rectum
8	chr1:174127600-174129800	Active TSS	H9 Cell Line	embryonic stem cell
9	chr1:174127600-174129800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:174127600-174129800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:174127600-174129800	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr1:174127600-174130000	Active TSS	H1 Cell Line	embryonic stem cell
13	chr1:174127600-174130000	Active TSS	Colonic Mucosa	Colon
14	chr1:174127600-174130000	Active TSS	NHDF-Ad	bronchial
15	chr1:174127600-174130000	Active TSS	NHLF	lung
16	chr1:174127600-174130200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:174127800-174129200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:174127800-174129200	Active TSS	Brain Hippocampus Middle	brain
19	chr1:174127800-174129200	Active TSS	Fetal Muscle Trunk	muscle
20	chr1:174127800-174129200	Active TSS	Placenta	Placenta
21	chr1:174127800-174129400	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr1:174127800-174129400	Active TSS	Right Ventricle	heart
23	chr1:174127800-174129400	Active TSS	Thymus	Thymus
24	chr1:174127800-174129400	Active TSS	A549	lung
25	chr1:174127800-174129600	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr1:174127800-174129600	Active TSS	Stomach Mucosa	stomach
27	chr1:174127800-174129800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr1:174127800-174129800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:174127800-174129800	Active TSS	Aorta	Aorta
30	chr1:174127800-174129800	Active TSS	Brain Substantia Nigra	brain
31	chr1:174127800-174129800	Active TSS	Psoas Muscle	Psoas
32	chr1:174127800-174129800	Active TSS	HSMM	muscle
33	chr1:174127800-174129800	Active TSS	HSMMtube	muscle
34	chr1:174127800-174130000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr1:174127800-174130000	Active TSS	Fetal Intestine Large	intestine
36	chr1:174127800-174130000	Active TSS	Placenta Amnion	Placenta Amnion
37	chr1:174127800-174130200	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr1:174128000-174128600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr1:174128000-174128800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:174128000-174129200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr1:174128000-174129200	Active TSS	Primary T cells fromperipheralblood	blood
42	chr1:174128000-174129200	Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr1:174128000-174129200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr1:174128000-174129200	Active TSS	Gastric	stomach
45	chr1:174128000-174129400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr1:174128000-174129400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:174128000-174129400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr1:174128000-174129400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
49	chr1:174128000-174129400	Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr1:174128000-174129400	Active TSS	Brain Cingulate Gyrus	brain

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