Variant report

Variant	rs2279630
Chromosome Location	chr3:194869342-194869343
allele	A/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	PAX5	chr3:194869212-194869546	GM12878	blood:	n/a	n/a
2	EP300	chr3:194868315-194869517	GM12878	blood:	n/a	chr3:194868557-194868571 chr3:194868347-194868361
3	POLR2A	chr3:194869140-194869678	GM12892	blood:	n/a	n/a
4	TBL1XR1	chr3:194868258-194869457	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:194868265-194872140	GM12891	blood:	n/a	n/a
6	POLR2A	chr3:194868269-194872203	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr3:194869199-194869594	GM12878	blood:	n/a	n/a
8	POLR2A	chr3:194868355-194872209	HUVEC	blood vessel:	n/a	n/a
9	CHD1	chr3:194868421-194871809	GM12878	blood:	n/a	n/a
10	POLR2A	chr3:194868228-194869817	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr3:194869180-194869573	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:194868151-194869746	GM12892	blood:	n/a	n/a
13	NFIC	chr3:194868131-194869898	GM12878	blood:	n/a	n/a
14	POLR2A	chr3:194868127-194869798	GM18505	blood:	n/a	n/a
15	POLR2A	chr3:194869182-194869538	GM12878	blood:	n/a	n/a
16	CHD2	chr3:194868295-194869605	GM12878	blood:	n/a	n/a
17	POLR2A	chr3:194869013-194869741	GM12891	blood:	n/a	n/a
18	POLR2A	chr3:194868262-194872259	HUVEC	blood vessel:	n/a	n/a
19	CREB1	chr3:194868198-194869920	GM12878	blood:	n/a	n/a
20	POLR2A	chr3:194868152-194869722	GM12892	blood:	n/a	n/a
21	POLR2A	chr3:194868310-194869727	GM12891	blood:	n/a	n/a
22	CEBPB	chr3:194868151-194869887	GM12878	blood:	n/a	n/a
23	BCLAF1	chr3:194868147-194869699	GM12878	blood:	n/a	chr3:194868557-194868566
24	ATF2	chr3:194868155-194869714	GM12878	blood:	n/a	n/a
25	TAF1	chr3:194869226-194869538	GM12891	blood:	n/a	n/a
26	EP300	chr3:194868261-194869438	GM12878	blood:	n/a	chr3:194868557-194868571 chr3:194868347-194868361
27	POLR2A	chr3:194868143-194869696	GM12891	blood:	n/a	n/a
28	POLR2A	chr3:194868129-194869750	GM12878	blood:	n/a	n/a
29	POLR2A	chr3:194868254-194869675	GM12891	blood:	n/a	n/a
30	PAX5	chr3:194869197-194869481	GM12878	blood:	n/a	n/a
31	STAT1	chr3:194869275-194869473	GM12878	blood:	n/a	n/a
32	BHLHE40	chr3:194869265-194869446	K562	blood:	n/a	n/a
33	MAZ	chr3:194868284-194869661	GM12878	blood:	n/a	n/a
34	RCOR1	chr3:194868255-194869750	GM12878	blood:	n/a	n/a
35	TBL1XR1	chr3:194869246-194869658	K562	blood:	n/a	n/a
36	JUND	chr3:194869328-194869731	K562	blood:	n/a	n/a
37	EBF1	chr3:194867799-194869562	GM12878	blood:	n/a	n/a
38	ATF2	chr3:194868151-194869739	GM12878	blood:	n/a	n/a
39	BCLAF1	chr3:194868142-194869693	GM12878	blood:	n/a	chr3:194868557-194868566
40	POLR2A	chr3:194868140-194869736	GM19193	blood:	n/a	n/a
41	STAT3	chr3:194868245-194869745	GM12878	blood:	n/a	n/a
42	POLR2A	chr3:194869063-194869679	GM12892	blood:	n/a	n/a
43	POLR2A	chr3:194868342-194871929	GM12878	blood:	n/a	n/a
44	POLR2A	chr3:194868149-194872233	HUVEC	blood vessel:	n/a	n/a
45	MTA3	chr3:194868157-194872051	GM12878	blood:	n/a	n/a
46	MYC	chr3:194869308-194869657	K562	blood:	n/a	n/a
47	POLR2A	chr3:194868129-194869701	GM12878	blood:	n/a	n/a
48	WRNIP1	chr3:194868286-194869675	GM12878	blood:	n/a	n/a
49	RUNX3	chr3:194869187-194869727	GM12878	blood:	n/a	n/a
50	MTA3	chr3:194869081-194869708	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:194868967..194870771-chr3:194979716..194982181,2	K562	blood:

Variant related genes	Relation type
RN7SL36P	TF binding region
ENSG00000173950	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11721261	0.80[EUR][1000 genomes]
rs11917068	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1552893	0.82[AMR][1000 genomes]
rs2172695	0.85[AMR][1000 genomes]
rs28573813	0.87[AMR][1000 genomes]
rs4266129	0.86[AMR][1000 genomes]
rs4300953	0.83[AMR][1000 genomes]
rs4645095	0.81[AMR][1000 genomes]
rs4677663	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4677812	0.90[AMR][1000 genomes]
rs4677818	0.89[AFR][1000 genomes]
rs58370605	0.81[AMR][1000 genomes]
rs60329099	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6794540	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7612579	0.85[AMR][1000 genomes]
rs7639698	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7646496	0.91[AMR][1000 genomes]
rs903310	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs950257	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv997779	chr3:194687093-194885936	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv536874	chr3:194687093-194885936	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
6	nsv1012592	chr3:194814446-194931562	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
7	nsv536875	chr3:194814446-194931562	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
8	nsv1001492	chr3:194814990-194935397	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
9	nsv461126	chr3:194817484-194961888	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
10	nsv592981	chr3:194817484-194961888	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
11	nsv878137	chr3:194822098-194900432	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
12	nsv461127	chr3:194833940-194934634	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
13	nsv592982	chr3:194833940-194934634	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
14	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
15	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
16	nsv533904	chr3:194868329-195438728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194841000-194872800	Weak transcription	HSMMtube	muscle
2	chr3:194854600-194871000	Weak transcription	Fetal Brain Female	brain
3	chr3:194860800-194870200	Weak transcription	Right Ventricle	heart
4	chr3:194861000-194881000	Weak transcription	Hela-S3	cervix
5	chr3:194861200-194872600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:194861600-194870800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:194861800-194870800	Weak transcription	Aorta	Aorta
8	chr3:194861800-194871000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:194861800-194871200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:194861800-194872800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:194861800-194875000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:194862400-194870600	Weak transcription	Osteobl	bone
13	chr3:194862400-194897800	Weak transcription	Dnd41	blood
14	chr3:194863000-194869400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:194863800-194870200	Weak transcription	Ovary	ovary
16	chr3:194864400-194870800	Weak transcription	Brain Angular Gyrus	brain
17	chr3:194865000-194871000	Enhancers	Fetal Thymus	thymus
18	chr3:194866600-194870200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:194866800-194870600	Enhancers	K562	blood
20	chr3:194867200-194871800	Enhancers	Spleen	Spleen
21	chr3:194867400-194870000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr3:194867400-194871000	Weak transcription	Brain Substantia Nigra	brain
23	chr3:194867600-194869400	Enhancers	Placenta	Placenta
24	chr3:194867600-194871000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr3:194867800-194870000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:194867800-194872000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:194867800-194872400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:194868000-194870000	Active TSS	GM12878-XiMat	blood
29	chr3:194868000-194870400	Active TSS	Rectal Smooth Muscle	rectum
30	chr3:194868000-194870800	Weak transcription	Brain Hippocampus Middle	brain
31	chr3:194868200-194869400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr3:194868200-194869400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
33	chr3:194868200-194869400	Active TSS	Colon Smooth Muscle	Colon
34	chr3:194868200-194869600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
35	chr3:194868200-194869600	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr3:194868200-194869600	Active TSS	Stomach Smooth Muscle	stomach
37	chr3:194868200-194870200	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr3:194868200-194871000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:194868200-194871400	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr3:194868200-194871800	Active TSS	Rectal Mucosa Donor 29	rectum
41	chr3:194868200-194872000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr3:194868200-194872200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
43	chr3:194868200-194872200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:194868200-194877800	Enhancers	Fetal Stomach	stomach
45	chr3:194868400-194869600	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr3:194868400-194869800	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr3:194868400-194870800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr3:194868400-194870800	Enhancers	Fetal Lung	lung
49	chr3:194868400-194871000	Enhancers	H1 Cell Line	embryonic stem cell
50	chr3:194868400-194871000	Enhancers	HUES6 Cell Line	embryonic stem cell

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