Variant report

Variant	rs3749400
Chromosome Location	chr3:150128484-150128485
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	MAX	chr3:150125067-150129102	A549	lung:	n/a	chr3:150125747-150125757
2	POLR2A	chr3:150128218-150128688	A549	lung:	n/a	n/a
3	MXI1	chr3:150125032-150131571	SK-N-SH	brain:	n/a	chr3:150130450-150130459
4	POLR2A	chr3:150125375-150129053	Hela-S3	cervix:	n/a	n/a
5	CTCF	chr3:150127255-150129086	SK-N-SH	brain:	n/a	n/a
6	CTCF	chr3:150128420-150128570	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr3:150124821-150129086	SK-N-MC	brain:	n/a	n/a
8	RAD21	chr3:150126996-150129135	SK-N-SH	brain:	n/a	n/a
9	JUN	chr3:150124199-150130937	K562	blood:	n/a	chr3:150126610-150126621 chr3:150126364-150126373 chr3:150126007-150126016 chr3:150126003-150126016 chr3:150125540-150125551 chr3:150125537-150125549 chr3:150130480-150130492 chr3:150127088-150127099
10	MAX	chr3:150125252-150128931	NB4	blood:	n/a	chr3:150125747-150125757
11	POLR2A	chr3:150125260-150128683	K562	blood:	n/a	n/a
12	SIN3AK20	chr3:150125736-150129137	MCF-7	breast:	n/a	n/a
13	POLR2A	chr3:150128064-150129530	A549	lung:	n/a	n/a
14	POLR2A	chr3:150125575-150128772	K562	blood:	n/a	n/a
15	MAX	chr3:150127413-150128821	K562	blood:	n/a	n/a
16	POLR2A	chr3:150127392-150129039	GM12892	blood:	n/a	n/a
17	POLR2A	chr3:150127489-150129150	H1-neurons	neurons:	n/a	n/a
18	POLR2A	chr3:150125311-150128930	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:150128452-150128791	GM12878	blood:	n/a	n/a
20	SIN3AK20	chr3:150125117-150129299	MCF-7	breast:	n/a	n/a
21	POLR2A	chr3:150125736-150128935	MCF-7	breast:	n/a	n/a
22	POLR2A	chr3:150125121-150129116	PBDE	blood:	n/a	n/a
23	MYC	chr3:150127553-150129010	K562	blood:	n/a	n/a
24	SIN3AK20	chr3:150128480-150129147	SK-N-SH	brain:	n/a	n/a
25	TCF12	chr3:150125241-150128915	A549	lung:	n/a	chr3:150125660-150125667
26	POLR2A	chr3:150128385-150128848	HUVEC	blood vessel:	n/a	n/a
27	POLR2A	chr3:150125769-150128897	MCF-7	breast:	n/a	n/a
28	MAX	chr3:150125539-150129083	MCF-7	breast:	n/a	chr3:150125747-150125757
29	MYC	chr3:150127699-150129032	MCF10A-Er-Src	breast:	n/a	n/a
30	TAF1	chr3:150127617-150128758	HepG2	liver:	n/a	n/a
31	UBTF	chr3:150125471-150129388	K562	blood:	n/a	n/a
32	MYC	chr3:150128452-150128829	MCF-7	breast:	n/a	n/a
33	JUND	chr3:150124892-150128974	SK-N-SH	brain:	n/a	chr3:150126610-150126621 chr3:150126364-150126373 chr3:150126007-150126016 chr3:150125540-150125551 chr3:150125537-150125549 chr3:150127088-150127099
34	MAX	chr3:150125878-150128627	K562	blood:	n/a	n/a
35	POLR2A	chr3:150125448-150128553	GM15510	blood:	n/a	n/a
36	POLR2A	chr3:150125317-150129290	Hela-S3	cervix:	n/a	n/a
37	MAX	chr3:150127549-150129046	A549	lung:	n/a	n/a
38	POLR2A	chr3:150125206-150129913	K562	blood:	n/a	n/a
39	MAX	chr3:150127655-150128916	H1-hESC	embryonic stem cell:	n/a	n/a
40	RCOR1	chr3:150128435-150129055	Hela-S3	cervix:	n/a	n/a
41	SMARCB1	chr3:150125951-150128961	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr3:150127537-150128940	GM12892	blood:	n/a	n/a
43	MYC	chr3:150128187-150128857	MCF-7	breast:	n/a	n/a
44	MXI1	chr3:150127549-150129505	Hela-S3	cervix:	n/a	n/a
45	HCFC1	chr3:150124974-150130064	Hela-S3	cervix:	n/a	n/a
46	TFAP2C	chr3:150125966-150129016	Hela-S3	cervix:	n/a	chr3:150126458-150126473 chr3:150126438-150126453
47	POLR2A	chr3:150127940-150129043	MCF-7	breast:	n/a	n/a
48	POLR2A	chr3:150124838-150130078	PANC-1	pancreas:	n/a	n/a
49	POLR2A	chr3:150125394-150128794	Raji	blood:	n/a	n/a
50	SMC3	chr3:150125357-150129105	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:149953695..149960076-chr3:150124777..150129995,22	MCF-7	breast:
2	chr3:150106944..150109021-chr3:150126806..150128575,2	K562	blood:
3	chr3:150002946..150005650-chr3:150125289..150128542,3	K562	blood:
4	chr3:150122822..150130151-chr3:150261910..150267967,8	K562	blood:
5	chr3:150124697..150131961-chr3:150259924..150266159,12	MCF-7	breast:
6	chr3:150124105..150129008-chr3:150174357..150179992,6	MCF-7	breast:
7	chr3:150121790..150130149-chr3:150138506..150143439,10	MCF-7	breast:
8	chr3:150003406..150008220-chr3:150125314..150128917,4	K562	blood:
9	chr3:150126707..150128602-chr3:150209463..150211558,2	MCF-7	breast:
10	chr3:150125257..150128558-chr3:150478258..150482422,4	K562	blood:
11	chr3:150030571..150033361-chr3:150126551..150128588,2	K562	blood:
12	chr3:150003129..150006271-chr3:150124947..150129304,6	MCF-7	breast:
13	chr3:150097794..150100688-chr3:150126424..150128739,2	K562	blood:
14	chr3:149953873..149961412-chr3:150123750..150131229,19	MCF-7	breast:

Variant related genes	Relation type
TSC22D2	TF binding region
ENSG00000243550	Chromatin interaction
ENSG00000120742	Chromatin interaction
ENSG00000244541	Chromatin interaction
ENSG00000144895	Chromatin interaction
ENSG00000181788	Chromatin interaction
ENSG00000244265	Chromatin interaction
ENSG00000196428	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10513368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10513369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10513370	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10513371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10513372	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10513375	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11713072	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714034	0.94[EUR][1000 genomes]
rs11714123	1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs11925759	0.86[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11928577	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11928948	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13066114	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13067910	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13068946	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13073230	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs13076419	0.85[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13089766	0.87[EUR][1000 genomes]
rs13317818	0.93[ASN][1000 genomes]
rs1376027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17278131	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs28571974	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28587291	0.93[ASN][1000 genomes]
rs2868430	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34106738	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34156311	0.96[ASN][1000 genomes]
rs34419133	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34503712	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34647320	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34983941	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35019980	0.87[EUR][1000 genomes]
rs35234277	0.86[ASN][1000 genomes]
rs35598887	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3811719	0.93[ASN][1000 genomes]
rs61734437	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66816665	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67073112	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67100311	0.87[EUR][1000 genomes]
rs6791546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799106	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73165716	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73167540	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7614772	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7618493	0.93[ASN][1000 genomes]
rs7620193	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7621019	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7623100	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9827736	0.86[ASN][1000 genomes]
rs9844735	0.93[ASN][1000 genomes]
rs9875752	0.93[ASN][1000 genomes]
rs9879140	0.93[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	nsv829755	chr3:149992023-150156001	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	esv1828464	chr3:150096071-150149868	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv877645	chr3:150103135-150212698	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	esv1818335	chr3:150122121-150128717	Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	esv14316	chr3:150124574-150128485	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	43 gene(s)	inside rSNPs	diseases
6	esv1799287	chr3:150125721-150147118	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 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	chr3:150124600-150130600	Active TSS	Aorta	Aorta
2	chr3:150124600-150132200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr3:150124600-150133000	Active TSS	Fetal Kidney	kidney
4	chr3:150124600-150133000	Active TSS	Right Atrium	heart
5	chr3:150124800-150128600	Active TSS	HSMM	muscle
6	chr3:150124800-150128800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:150124800-150129200	Active TSS	Primary T killer memory cells from peripheral blood	blood
8	chr3:150124800-150133600	Active TSS	Stomach Smooth Muscle	stomach
9	chr3:150125000-150128600	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr3:150125000-150128600	Active TSS	Fetal Muscle Trunk	muscle
11	chr3:150125000-150128600	Active TSS	Fetal Muscle Leg	muscle
12	chr3:150125000-150128600	Active TSS	K562	blood
13	chr3:150125000-150129200	Active TSS	Brain Substantia Nigra	brain
14	chr3:150125000-150129200	Active TSS	Duodenum Mucosa	Duodenum
15	chr3:150125000-150130200	Active TSS	Brain Anterior Caudate	brain
16	chr3:150125000-150130400	Active TSS	Liver	Liver
17	chr3:150125000-150130600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:150125000-150130600	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr3:150125000-150130600	Active TSS	Psoas Muscle	Psoas
20	chr3:150125000-150130800	Active TSS	Rectal Smooth Muscle	rectum
21	chr3:150125000-150131200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
22	chr3:150125000-150131200	Active TSS	Placenta	Placenta
23	chr3:150125000-150131600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:150125000-150132400	Active TSS	Fetal Stomach	stomach
25	chr3:150125000-150132600	Active TSS	HSMMtube	muscle
26	chr3:150125000-150132800	Active TSS	Fetal Intestine Large	intestine
27	chr3:150125000-150133200	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr3:150125000-150137400	Active TSS	GM12878-XiMat	blood
29	chr3:150125200-150128600	Active TSS	Primary T cells fromperipheralblood	blood
30	chr3:150125200-150128600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
31	chr3:150125200-150128600	Active TSS	Sigmoid Colon	Sigmoid Colon
32	chr3:150125200-150128600	Active TSS	A549	lung
33	chr3:150125200-150128600	Active TSS	NHDF-Ad	bronchial
34	chr3:150125200-150128800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:150125200-150128800	Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr3:150125200-150129600	Active TSS	Fetal Brain Female	brain
37	chr3:150125200-150130600	Active TSS	Colon Smooth Muscle	Colon
38	chr3:150125200-150130600	Active TSS	Left Ventricle	heart
39	chr3:150125200-150130600	Active TSS	Ovary	ovary
40	chr3:150125200-150131200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr3:150125200-150131200	Active TSS	H9 Cell Line	embryonic stem cell
42	chr3:150125200-150131200	Active TSS	Stomach Mucosa	stomach
43	chr3:150125200-150132400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr3:150125200-150132400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr3:150125400-150128600	Active TSS	Esophagus	oesophagus
46	chr3:150125400-150128600	Active TSS	Placenta Amnion	Placenta Amnion
47	chr3:150125400-150128600	Active TSS	HMEC	breast
48	chr3:150125400-150128600	Active TSS	NHEK	skin
49	chr3:150125400-150128800	Active TSS	Thymus	Thymus
50	chr3:150125400-150128800	Active TSS	Monocytes-CD14+_RO01746	blood

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