Variant report

Variant	rs4997276
Chromosome Location	chr1:209943787-209943788
allele	G/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	POLR2A	chr1:209941568-209945214	GM18951	blood:	n/a	n/a
2	STAT5A	chr1:209943577-209945094	GM12878	blood:	n/a	n/a
3	MAX	chr1:209943647-209943801	GM12878	blood:	n/a	n/a
4	CTCF	chr1:209943716-209943833	GM12892	blood:	n/a	n/a
5	MAX	chr1:209941095-209944027	NB4	blood:	n/a	chr1:209943038-209943048 chr1:209943557-209943567
6	POLR2A	chr1:209941537-209945106	GM12892	blood:	n/a	n/a
7	EP300	chr1:209942216-209943822	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr1:209940700-209952492	GM12891	blood:	n/a	n/a
9	MTA3	chr1:209942612-209943814	GM12878	blood:	n/a	n/a
10	TCF12	chr1:209942145-209943901	SK-N-SH	brain:	n/a	chr1:209943560-209943570
11	POLR2A	chr1:209941560-209945629	GM12878	blood:	n/a	n/a
12	POU2F2	chr1:209943526-209944502	GM12878	blood:	n/a	n/a
13	MEF2A	chr1:209942334-209943787	SK-N-SH	brain:	n/a	chr1:209942839-209942854 chr1:209942838-209942859 chr1:209942840-209942854
14	EP300	chr1:209942218-209943867	SK-N-SH	brain:	n/a	n/a
15	CTCF	chr1:209943655-209945439	GM19239	blood:	n/a	n/a
16	POLR2A	chr1:209943562-209945093	HL-60	blood:	n/a	n/a
17	CTCF	chr1:209943660-209943810	GM12872	blood:	n/a	n/a
18	SUZ12	chr1:209943709-209944071	H1-hESC	embryonic stem cell:	n/a	n/a
19	MTA3	chr1:209941494-209944028	GM12878	blood:	n/a	n/a
20	POLR2A	chr1:209941574-209945063	GM12878	blood:	n/a	n/a
21	CTCF	chr1:209943680-209943830	GM12872	blood:	n/a	n/a
22	POLR2A	chr1:209941567-209945023	GM18526	blood:	n/a	n/a
23	POLR2A	chr1:209943512-209945521	GM12891	blood:	n/a	n/a
24	POLR2A	chr1:209941117-209946709	GM18505	blood:	n/a	n/a
25	POLR2A	chr1:209942381-209945631	GM12892	blood:	n/a	n/a
26	GATA3	chr1:209942300-209943875	SK-N-SH	brain:	n/a	chr1:209942977-209942987
27	POLR2A	chr1:209943616-209945450	GM12878	blood:	n/a	n/a
28	POLR2A	chr1:209943490-209943877	GM12878	blood:	n/a	n/a
29	POLR2A	chr1:209941509-209947286	GM12878	blood:	n/a	n/a
30	POLR2A	chr1:209943536-209945521	GM12891	blood:	n/a	n/a
31	POLR2A	chr1:209941597-209945746	GM19099	blood:	n/a	n/a
32	POLR2A	chr1:209941520-209945190	GM15510	blood:	n/a	n/a
33	NR2C2	chr1:209943704-209945090	GM12878	blood:	n/a	n/a
34	POLR2A	chr1:209942360-209945616	GM12892	blood:	n/a	n/a
35	ZEB1	chr1:209943163-209945525	GM12878	blood:	n/a	n/a
36	POLR2A	chr1:209942521-209944174	GM12878	blood:	n/a	n/a
37	POLR2A	chr1:209943578-209945455	GM12891	blood:	n/a	n/a
38	STAT5A	chr1:209942515-209946308	GM12878	blood:	n/a	chr1:209942981-209942989 chr1:209942982-209942994 chr1:209945841-209945853 chr1:209943537-209943545
39	POLR2A	chr1:209942422-209945671	GM12892	blood:	n/a	n/a
40	POLR2A	chr1:209943659-209945080	GM12878	blood:	n/a	n/a
41	POLR2A	chr1:209943517-209945479	GM12892	blood:	n/a	n/a
42	POLR2A	chr1:209943573-209945492	GM12878	blood:	n/a	n/a
43	GATA3	chr1:209942251-209943892	SK-N-SH	brain:	n/a	chr1:209942977-209942987
44	POLR2A	chr1:209943578-209944728	GM12891	blood:	n/a	n/a
45	ZEB1	chr1:209943523-209945114	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:209931478..209933302-chr1:209941660..209944063,2	K562	blood:
2	chr1:209943015..209945017-chr1:209946674..209949825,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HSD11B1-4	chr1:209943366-209944059	NONHSAT009235
2	lnc-HSD11B1-4	chr1:209943562-209944045	NONHSAT009236
3	lnc-HSD11B1-4	chr1:209943622-209943813	NONHSAT009237
4	lnc-HSD11B1-4	chr1:209943688-209943793	NONHSAT009238
5	lnc-C1orf74-2	chr1:209943688-209943821	NONHSAT009239

Variant related genes	Relation type
TRAF3IP3	TF binding region
ENSG00000009790	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs17015239	1.00[AMR][1000 genomes]
rs17015257	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription 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	27 gene(s)	inside rSNPs	diseases
4	nsv1006632	chr1:209886202-209970355	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv4343	chr1:209929932-209974877	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	esv3429215	chr1:209942329-209947327	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv3449118	chr1:209942529-209946727	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
8	esv3393757	chr1:209943129-209946427	Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
9	esv3375148	chr1:209943179-209945677	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
10	esv3391985	chr1:209943579-209946077	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209940600-209944200	Flanking Active TSS	Dnd41	blood
2	chr1:209940800-209943800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:209940800-209943800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
4	chr1:209940800-209944000	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr1:209940800-209944000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:209940800-209944000	Enhancers	HMEC	breast
7	chr1:209940800-209946200	Enhancers	Fetal Stomach	stomach
8	chr1:209941000-209944000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
9	chr1:209941000-209945800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:209941400-209943800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:209941400-209943800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:209941400-209943800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr1:209941400-209944200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
14	chr1:209941400-209944400	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr1:209941400-209945000	Flanking Active TSS	GM12878-XiMat	blood
16	chr1:209941600-209943800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:209941600-209943800	Enhancers	Brain Hippocampus Middle	brain
18	chr1:209941600-209943800	Enhancers	Fetal Muscle Leg	muscle
19	chr1:209941600-209944000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:209941600-209944200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
21	chr1:209941600-209944400	Active TSS	Primary T helper naive cells from peripheral blood	blood
22	chr1:209941600-209944400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr1:209941800-209943800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:209941800-209943800	Active TSS	Primary T killer memory cells from peripheral blood	blood
25	chr1:209941800-209944000	Flanking Active TSS	Stomach Smooth Muscle	stomach
26	chr1:209941800-209944600	Flanking Active TSS	Rectal Smooth Muscle	rectum
27	chr1:209941800-209944800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:209941800-209945000	Enhancers	Left Ventricle	heart
29	chr1:209942000-209943800	Enhancers	Pancreas	Pancrea
30	chr1:209942000-209943800	Active TSS	Sigmoid Colon	Sigmoid Colon
31	chr1:209942000-209944000	Enhancers	Brain Cingulate Gyrus	brain
32	chr1:209942000-209944000	Enhancers	HUVEC	blood vessel
33	chr1:209942000-209944200	Enhancers	NHLF	lung
34	chr1:209942000-209944800	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr1:209942000-209944800	Enhancers	Brain Substantia Nigra	brain
36	chr1:209942000-209945400	Enhancers	Placenta	Placenta
37	chr1:209942200-209943800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:209942200-209943800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr1:209942200-209943800	Enhancers	Spleen	Spleen
40	chr1:209942400-209943800	Active TSS	Primary T cells fromperipheralblood	blood
41	chr1:209942400-209944200	Enhancers	NHDF-Ad	bronchial
42	chr1:209942400-209944600	Flanking Active TSS	Fetal Thymus	thymus
43	chr1:209942600-209943800	Active TSS	Liver	Liver
44	chr1:209942800-209943800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:209942800-209943800	Active TSS	Primary T cells from cord blood	blood
46	chr1:209942800-209943800	Weak transcription	Fetal Kidney	kidney
47	chr1:209942800-209944000	Enhancers	NH-A	brain
48	chr1:209942800-209944600	Enhancers	Fetal Muscle Trunk	muscle
49	chr1:209942800-209956800	Weak transcription	Small Intestine	intestine
50	chr1:209942800-209957200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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