Variant report

Variant	rs3806243
Chromosome Location	chr1:185126866-185126867
allele	A/C
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	POLR2A	chr1:185125059-185127295	HepG2	liver:	n/a	n/a
2	SP1	chr1:185125669-185126951	A549	lung:	n/a	chr1:185126230-185126242 chr1:185126357-185126366 chr1:185126564-185126573 chr1:185126499-185126512 chr1:185126357-185126366 chr1:185126356-185126365 chr1:185126562-185126574 chr1:185126230-185126242 chr1:185126498-185126507 chr1:185126380-185126392 chr1:185126232-185126241 chr1:185126377-185126391 chr1:185126231-185126241 chr1:185126231-185126241 chr1:185126381-185126390 chr1:185126562-185126574 chr1:185126227-185126241 chr1:185126580-185126590 chr1:185126356-185126366 chr1:185126355-185126367 chr1:185126563-185126572 chr1:185126231-185126240 chr1:185126232-185126241 chr1:185126230-185126241 chr1:185126497-185126506 chr1:185126226-185126239
3	TEAD4	chr1:185124883-185126937	K562	blood:	n/a	n/a
4	ETS1	chr1:185125476-185126949	A549	lung:	n/a	chr1:185126254-185126269 chr1:185126325-185126338 chr1:185126257-185126271 chr1:185126229-185126240 chr1:185126258-185126265
5	GABPA	chr1:185125658-185126904	SK-N-SH	brain:	n/a	chr1:185126231-185126240
6	POLR2A	chr1:185124997-185127327	K562	blood:	n/a	n/a
7	POLR2A	chr1:185125207-185126930	PFSK-1	brain:	n/a	n/a
8	POLR2A	chr1:185125727-185126919	HCT-116	colon:	n/a	n/a
9	CBX3	chr1:185124980-185126908	K562	blood:	n/a	n/a
10	SPI1	chr1:185126831-185127155	GM12878	blood:	n/a	n/a
11	POLR2A	chr1:185125080-185126876	HepG2	liver:	n/a	n/a
12	MXI1	chr1:185124961-185127085	GM12878	blood:	n/a	n/a
13	ZNF143	chr1:185125889-185126873	K562	blood:	n/a	chr1:185126327-185126345 chr1:185126329-185126338 chr1:185126331-185126350 chr1:185126432-185126442 chr1:185126207-185126222
14	POLR2A	chr1:185125523-185126880	Gliobla	brain:	n/a	n/a
15	RFX5	chr1:185124285-185127206	SK-N-SH	brain:	n/a	chr1:185126852-185126860 chr1:185125214-185125231
16	NR2F2	chr1:185125316-185127328	K562	blood:	n/a	n/a
17	SIN3A	chr1:185125940-185127093	GM12878	blood:	n/a	n/a
18	MAX	chr1:185125616-185126921	SK-N-SH	brain:	n/a	n/a
19	SREBP1	chr1:185124548-185127215	GM12878	blood:	n/a	n/a
20	TBP	chr1:185125492-185127067	H1-hESC	embryonic stem cell:	n/a	n/a
21	BCLAF1	chr1:185125237-185126928	GM12878	blood:	n/a	chr1:185126692-185126705 chr1:185126497-185126506 chr1:185126684-185126697
22	POLR2A	chr1:185125669-185126924	U87	brain:	n/a	n/a
23	HEY1	chr1:185125767-185127236	K562	blood:	n/a	chr1:185126689-185126704 chr1:185125875-185125890 chr1:185125884-185125899
24	POLR2A	chr1:185125264-185127050	Hela-S3	cervix:	n/a	n/a
25	RELA	chr1:185125030-185126882	GM15510	blood:	n/a	n/a
26	SMARCB1	chr1:185125340-185127228	Hela-S3	cervix:	n/a	n/a
27	BCLAF1	chr1:185125309-185127012	GM12878	blood:	n/a	chr1:185126692-185126705 chr1:185126497-185126506 chr1:185126684-185126697
28	TCF7L2	chr1:185125281-185127266	Hela-S3	cervix:	n/a	n/a
29	MXI1	chr1:185126011-185126900	K562	blood:	n/a	n/a
30	POLR2A	chr1:185125049-185126899	GM12892	blood:	n/a	n/a
31	POLR2A	chr1:185125265-185127208	K562	blood:	n/a	n/a
32	POLR2A	chr1:185126531-185126937	GM12891	blood:	n/a	n/a
33	SMC3	chr1:185126815-185127092	GM12878	blood:	n/a	n/a
34	POLR2A	chr1:185125379-185126911	A549	lung:	n/a	n/a
35	SIN3A	chr1:185125055-185127329	H1-hESC	embryonic stem cell:	n/a	chr1:185127300-185127314
36	POLR2A	chr1:185125276-185127008	HUVEC	blood vessel:	n/a	n/a
37	CHD2	chr1:185125515-185127235	K562	blood:	n/a	chr1:185126357-185126367
38	POLR2A	chr1:185125600-185126924	U87	brain:	n/a	n/a
39	POLR2A	chr1:185125310-185127192	K562	blood:	n/a	n/a
40	MYC	chr1:185125272-185126874	K562	blood:	n/a	n/a
41	POLR2A	chr1:185124972-185126950	GM12878	blood:	n/a	n/a
42	POLR2A	chr1:185124935-185126904	GM18526	blood:	n/a	n/a
43	POLR2A	chr1:185125034-185126950	H1-neurons	neurons:	n/a	n/a
44	SIN3AK20	chr1:185125659-185126903	PANC-1	pancreas:	n/a	n/a
45	POLR2A	chr1:185125054-185127242	K562	blood:	n/a	n/a
46	POLR2A	chr1:185124891-185127136	GM12891	blood:	n/a	n/a
47	POLR2A	chr1:185125122-185126875	GM12878	blood:	n/a	n/a
48	STAT5A	chr1:185126716-185127215	GM12878	blood:	n/a	n/a
49	IRF1	chr1:185125848-185126919	K562	blood:	n/a	chr1:185126579-185126593 chr1:185126022-185126036 chr1:185126822-185126835 chr1:185126021-185126033 chr1:185126022-185126032 chr1:185126230-185126244 chr1:185126816-185126828
50	TBP	chr1:185125019-185127261	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:185013842..185016800-chr1:185124120..185127493,5	MCF-7	breast:
2	chr1:185124219..185126981-chr17:56736223..56737982,2	MCF-7	breast:
3	chr1:185124700..185128224-chr1:185139265..185140988,3	K562	blood:
4	chr1:185124212..185128355-chr1:185283797..185287901,7	K562	blood:
5	chr1:184721859..184724654-chr1:185126581..185128573,2	MCF-7	breast:
6	chr1:185012738..185017820-chr1:185123187..185127311,9	K562	blood:
7	chr1:185125770..185127987-chr1:185284886..185287172,2	MCF-7	breast:
8	chr1:184941281..184944338-chr1:185124829..185129491,4	K562	blood:
9	chr1:184941416..184944338-chr1:185125198..185127765,2	K562	blood:
10	chr1:185124975..185127830-chr1:185279297..185282140,2	K562	blood:
11	chr1:185124212..185127675-chr1:185284433..185287801,3	K562	blood:
12	chr1:185124896..185128464-chr1:185139300..185142346,3	MCF-7	breast:
13	chr1:185012738..185016714-chr1:185123889..185127545,9	K562	blood:

Variant related genes	Relation type
TRMT1L	TF binding region
ENSG00000231084	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000116406	Chromatin interaction
ENSG00000116679	Chromatin interaction
ENSG00000273004	Chromatin interaction
ENSG00000135842	Chromatin interaction
ENSG00000121481	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1008502	1.00[CEU][hapmap]
rs1046592	1.00[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs10489581	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs10797997	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes]
rs10797998	1.00[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs10911676	0.81[EUR][1000 genomes]
rs10911682	0.88[EUR][1000 genomes]
rs10911686	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12022419	1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs12023744	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12025995	0.93[EUR][1000 genomes]
rs12026000	0.93[EUR][1000 genomes]
rs12027607	0.86[AMR][1000 genomes]
rs12028809	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12030778	0.93[EUR][1000 genomes]
rs12030967	0.85[EUR][1000 genomes]
rs12031837	0.93[EUR][1000 genomes]
rs12035073	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs12035433	0.93[EUR][1000 genomes]
rs12037466	0.86[EUR][1000 genomes]
rs12037692	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs12039541	0.86[EUR][1000 genomes]
rs12040650	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes]
rs12041374	0.93[EUR][1000 genomes]
rs12043427	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs12043495	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs12043561	0.93[EUR][1000 genomes]
rs12043617	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs12044161	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12044997	0.85[EUR][1000 genomes]
rs12045772	0.85[EUR][1000 genomes]
rs12046095	0.93[EUR][1000 genomes]
rs12046202	0.85[EUR][1000 genomes]
rs12046801	0.81[EUR][1000 genomes]
rs12064938	0.82[AMR][1000 genomes]
rs12086086	1.00[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs12094983	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes]
rs12401293	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12404644	1.00[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs12408279	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs12408500	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12409926	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs1407554	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1544052	1.00[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs16865296	0.85[EUR][1000 genomes]
rs2273881	0.98[EUR][1000 genomes]
rs3766719	1.00[GIH][hapmap]
rs3766720	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs3766723	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap]
rs41264588	0.88[EUR][1000 genomes]
rs41264590	0.93[EUR][1000 genomes]
rs56107433	0.93[EUR][1000 genomes]
rs61125463	0.93[EUR][1000 genomes]
rs61495015	0.93[EUR][1000 genomes]
rs72724103	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72724108	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72739677	0.86[AMR][1000 genomes]
rs72741807	0.93[EUR][1000 genomes]
rs72741808	0.93[EUR][1000 genomes]
rs72741816	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72741817	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72741819	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[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	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv548396	chr1:185038104-185151378	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv521613	chr1:185071831-185171869	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 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	chr1:185124000-185127400	Active TSS	K562	blood
2	chr1:185124200-185127600	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr1:185124200-185128000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:185124400-185127600	Active TSS	Colonic Mucosa	Colon
5	chr1:185124600-185127000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:185124600-185127000	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr1:185124600-185127200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:185124600-185127400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:185124600-185127400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:185124600-185127400	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr1:185124600-185127400	Active TSS	Fetal Lung	lung
12	chr1:185124600-185127400	Active TSS	A549	lung
13	chr1:185124600-185127600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:185124600-185127600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:185124600-185127600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:185124600-185127600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:185124600-185127600	Active TSS	Fetal Intestine Small	intestine
18	chr1:185124600-185127600	Active TSS	NHDF-Ad	bronchial
19	chr1:185124600-185127800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:185124600-185127800	Active TSS	GM12878-XiMat	blood
21	chr1:185124600-185127800	Active TSS	NHLF	lung
22	chr1:185124800-185127000	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr1:185124800-185127000	Active TSS	Primary B cells from peripheral blood	blood
24	chr1:185124800-185127000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:185124800-185127400	Active TSS	H9 Cell Line	embryonic stem cell
26	chr1:185124800-185127400	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr1:185124800-185127400	Active TSS	Aorta	Aorta
28	chr1:185124800-185127400	Active TSS	Duodenum Mucosa	Duodenum
29	chr1:185124800-185127400	Active TSS	Fetal Intestine Large	intestine
30	chr1:185124800-185127400	Active TSS	Fetal Stomach	stomach
31	chr1:185124800-185127400	Active TSS	Sigmoid Colon	Sigmoid Colon
32	chr1:185124800-185127400	Active TSS	HSMM	muscle
33	chr1:185124800-185127600	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr1:185124800-185127600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:185124800-185127600	Active TSS	Colon Smooth Muscle	Colon
36	chr1:185124800-185127600	Active TSS	Psoas Muscle	Psoas
37	chr1:185124800-185127600	Active TSS	Right Ventricle	heart
38	chr1:185125000-185127200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr1:185125000-185127200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:185125000-185127200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
41	chr1:185125000-185127200	Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr1:185125000-185127200	Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr1:185125000-185127200	Active TSS	Stomach Smooth Muscle	stomach
44	chr1:185125000-185127400	Active TSS	H1 Cell Line	embryonic stem cell
45	chr1:185125000-185127400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr1:185125000-185127400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:185125000-185127400	Active TSS	Fetal Muscle Trunk	muscle
48	chr1:185125000-185127400	Active TSS	Gastric	stomach
49	chr1:185125000-185127400	Active TSS	Left Ventricle	heart
50	chr1:185125000-185127400	Active TSS	Pancreas	Pancrea

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