Variant report

Variant	rs11922330
Chromosome Location	chr3:19188805-19188806
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	ELF1	chr3:19188059-19189074	MCF-7	breast:	n/a	n/a
2	ELF1	chr3:19188283-19189163	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:19188087-19189045	MCF-7	breast:	n/a	n/a
4	TCF7L2	chr3:19188629-19188999	HEK293	kidney:	n/a	n/a
5	TCF7L2	chr3:19188197-19189061	MCF-7	breast:	n/a	n/a
6	ZNF143	chr3:19188627-19189149	H1-hESC	embryonic stem cell:	n/a	chr3:19188702-19188712
7	GABPA	chr3:19188081-19188844	K562	blood:	n/a	chr3:19188558-19188567 chr3:19188698-19188707
8	MAX	chr3:19188045-19189013	H1-hESC	embryonic stem cell:	n/a	chr3:19188459-19188469 chr3:19188596-19188606 chr3:19188259-19188268
9	CBX3	chr3:19188612-19188891	K562	blood:	n/a	n/a
10	GTF2F1	chr3:19188630-19188975	H1-hESC	embryonic stem cell:	n/a	n/a
11	RCOR1	chr3:19188037-19189564	K562	blood:	n/a	n/a
12	MAX	chr3:19188126-19189065	ECC-1	luminal epithelium:	n/a	chr3:19188459-19188469 chr3:19188596-19188606 chr3:19188259-19188268
13	CREB1	chr3:19188245-19188958	GM12878	blood:	n/a	n/a
14	GABPA	chr3:19188189-19189060	MCF-7	breast:	n/a	chr3:19188558-19188567 chr3:19188698-19188707
15	CREB1	chr3:19188177-19188935	H1-hESC	embryonic stem cell:	n/a	n/a
16	FOXA1	chr3:19188630-19188960	HepG2	liver:	n/a	n/a
17	FOXA1	chr3:19188641-19188953	T-47D	breast:	n/a	n/a
18	TCF12	chr3:19188692-19188871	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:19188068-19189170	H1-neurons	neurons:	n/a	n/a
20	RUNX3	chr3:19188719-19189087	GM12878	blood:	n/a	n/a
21	TAF1	chr3:19188570-19189216	H1-hESC	embryonic stem cell:	n/a	n/a
22	BACH1	chr3:19187912-19189751	H1-hESC	embryonic stem cell:	n/a	n/a
23	JUND	chr3:19188205-19189060	H1-hESC	embryonic stem cell:	n/a	chr3:19189001-19189010 chr3:19188412-19188421
24	MAX	chr3:19187994-19189038	MCF-7	breast:	n/a	chr3:19188459-19188469 chr3:19188596-19188606 chr3:19188259-19188268
25	MTA3	chr3:19188665-19189209	GM12878	blood:	n/a	n/a
26	FOXA2	chr3:19188676-19188880	HepG2	liver:	n/a	n/a
27	TCF12	chr3:19188353-19189077	ECC-1	luminal epithelium:	n/a	n/a
28	EP300	chr3:19188287-19188881	SK-N-SH_RA	brain:	n/a	chr3:19188784-19188794
29	RCOR1	chr3:19188754-19188929	GM12878	blood:	n/a	n/a
30	TCF12	chr3:19188557-19188962	H1-hESC	embryonic stem cell:	n/a	n/a
31	MAZ	chr3:19188090-19189231	IMR90	lung:	n/a	chr3:19188459-19188469 chr3:19188596-19188606 chr3:19188259-19188268
32	POLR2A	chr3:19187332-19190031	H1-hESC	embryonic stem cell:	n/a	n/a
33	MAZ	chr3:19188135-19189114	GM12878	blood:	n/a	chr3:19188459-19188469 chr3:19188596-19188606 chr3:19188259-19188268
34	POLR2A	chr3:19188639-19189065	H1-hESC	embryonic stem cell:	n/a	n/a
35	TCF3	chr3:19188693-19188846	GM12878	blood:	n/a	chr3:19188777-19188787
36	GABPA	chr3:19188128-19188812	SK-N-SH	brain:	n/a	chr3:19188558-19188567 chr3:19188698-19188707
37	POLR2A	chr3:19187975-19189068	H1-neurons	neurons:	n/a	n/a
38	FOXA1	chr3:19188621-19188892	HepG2	liver:	n/a	n/a
39	MXI1	chr3:19187274-19191415	SK-N-SH	brain:	n/a	n/a
40	ELF1	chr3:19188172-19189068	MCF-7	breast:	n/a	n/a
41	ELF1	chr3:19188569-19188917	HepG2	liver:	n/a	n/a
42	HDAC2	chr3:19188062-19189160	H1-hESC	embryonic stem cell:	n/a	chr3:19188784-19188793 chr3:19188794-19188808
43	HDAC2	chr3:19188616-19188820	H1-hESC	embryonic stem cell:	n/a	chr3:19188784-19188793 chr3:19188794-19188808
44	RUNX3	chr3:19188785-19189162	GM12878	blood:	n/a	n/a
45	CEBPB	chr3:19188494-19188910	H1-hESC	embryonic stem cell:	n/a	n/a
46	E2F6	chr3:19188481-19189023	A549	lung:	n/a	chr3:19188558-19188570 chr3:19188791-19188802 chr3:19188558-19188567 chr3:19188698-19188707
47	TCF12	chr3:19188486-19189150	H1-hESC	embryonic stem cell:	n/a	n/a
48	CTBP2	chr3:19188135-19189125	H1-hESC	embryonic stem cell:	n/a	n/a
49	MYC	chr3:19188049-19189057	K562	blood:	n/a	chr3:19188459-19188469 chr3:19188596-19188606 chr3:19188259-19188268
50	E2F6	chr3:19188580-19188914	A549	lung:	n/a	chr3:19188791-19188802 chr3:19188698-19188707

No.	Distal block	Cell Line	Cell type
1	chr3:19186809..19189745-chr3:19319779..19321476,2	K562	blood:
2	chr3:19185341..19187435-chr3:19187905..19189651,2	MCF-7	breast:
3	chr3:19188168..19190474-chr3:19988134..19989911,2	MCF-7	breast:

Variant related genes	Relation type
KCNH8	TF binding region
ENSG00000163576	Chromatin interaction
ENSG00000144566	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10510486	1.00[GIH][hapmap]
rs11914725	1.00[CEU][hapmap]
rs11915614	1.00[CEU][hapmap]
rs11915915	1.00[CEU][hapmap]
rs11916273	0.93[AMR][1000 genomes]
rs11917497	1.00[CEU][hapmap]
rs11917668	1.00[CEU][hapmap]
rs11918112	1.00[CEU][hapmap]
rs11918147	1.00[CEU][hapmap]
rs11918308	1.00[CEU][hapmap]
rs11918533	1.00[CEU][hapmap]
rs11918685	1.00[CEU][hapmap]
rs11919461	1.00[CEU][hapmap]
rs11923068	1.00[CEU][hapmap]
rs11923157	1.00[CEU][hapmap]
rs11923699	1.00[CEU][hapmap]
rs11924695	1.00[CEU][hapmap]
rs11925180	1.00[CEU][hapmap]
rs11925510	1.00[CEU][hapmap]
rs11926160	1.00[CEU][hapmap]
rs11926703	1.00[CEU][hapmap]
rs11927110	1.00[CEU][hapmap]
rs11927919	1.00[CEU][hapmap]
rs11929014	1.00[CEU][hapmap]
rs12108002	1.00[CEU][hapmap]
rs1493925	1.00[CEU][hapmap]
rs1551062	1.00[GIH][hapmap]
rs17005744	1.00[CEU][hapmap]
rs17005761	1.00[CEU][hapmap]
rs17005762	1.00[CEU][hapmap]
rs17005767	1.00[CEU][hapmap]
rs17005770	1.00[CEU][hapmap]
rs17005771	1.00[CEU][hapmap]
rs17005800	1.00[CEU][hapmap]
rs17005811	1.00[CEU][hapmap]
rs1901008	1.00[CEU][hapmap]
rs2122380	1.00[CEU][hapmap]
rs2363094	1.00[CEU][hapmap]
rs2363095	1.00[CEU][hapmap]
rs57554756	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6769519	1.00[CEU][hapmap]
rs6783211	1.00[CEU][hapmap]
rs7427695	1.00[CEU][hapmap]
rs7433172	1.00[CEU][hapmap]
rs7613079	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs7625953	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7626630	1.00[CEU][hapmap]
rs7627612	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7628012	1.00[CEU][hapmap]
rs7629339	1.00[CEU][hapmap]
rs7631821	0.85[AFR][1000 genomes]
rs7632339	1.00[CEU][hapmap]
rs7633856	1.00[GIH][hapmap]
rs7634126	1.00[CEU][hapmap]
rs7636919	1.00[CEU][hapmap]
rs7639506	1.00[CEU][hapmap]
rs7641298	1.00[CEU][hapmap]
rs7643919	1.00[CEU][hapmap]
rs7645122	1.00[CEU][hapmap]
rs7647965	1.00[CEU][hapmap]
rs7652572	1.00[CEU][hapmap]
rs9755604	1.00[CEU][hapmap]
rs9756893	1.00[CEU][hapmap];1.00[GIH][hapmap]

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	nsv517847	chr3:18845347-19483695	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1010123	chr3:18990307-19989504	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1004602	chr3:19031671-19930052	Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv536511	chr3:19031671-19930052	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19187400-19189200	Active TSS	Stomach Smooth Muscle	stomach
2	chr3:19187400-19194000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:19187600-19189000	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr3:19187600-19189200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:19187600-19189200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:19187600-19189400	Flanking Active TSS	Dnd41	blood
7	chr3:19187600-19189600	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr3:19187600-19190000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:19187600-19190400	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr3:19187600-19190600	Active TSS	Fetal Brain Female	brain
11	chr3:19187600-19191000	Active TSS	H1 Cell Line	embryonic stem cell
12	chr3:19187800-19189200	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:19187800-19189200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:19187800-19189200	Active TSS	Brain Anterior Caudate	brain
15	chr3:19187800-19189200	Active TSS	Brain Hippocampus Middle	brain
16	chr3:19187800-19189200	Active TSS	Duodenum Mucosa	Duodenum
17	chr3:19187800-19189200	Active TSS	Fetal Lung	lung
18	chr3:19187800-19189200	Active TSS	Rectal Smooth Muscle	rectum
19	chr3:19187800-19189200	Active TSS	GM12878-XiMat	blood
20	chr3:19187800-19189200	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
21	chr3:19187800-19189400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr3:19187800-19189400	Active TSS	Brain Cingulate Gyrus	brain
23	chr3:19187800-19189400	Active TSS	NHLF	lung
24	chr3:19187800-19189600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:19187800-19189600	Active TSS	K562	blood
26	chr3:19187800-19190000	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr3:19187800-19190200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr3:19187800-19190200	Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr3:19187800-19190200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:19187800-19190200	Active TSS	Fetal Kidney	kidney
31	chr3:19187800-19190600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:19187800-19190800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr3:19187800-19190800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr3:19187800-19190800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr3:19187800-19191000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:19187800-19191000	Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr3:19187800-19191400	Active TSS	H9 Cell Line	embryonic stem cell
38	chr3:19187800-19191400	Active TSS	Fetal Brain Male	brain
39	chr3:19187800-19191600	Active TSS	Brain Germinal Matrix	brain
40	chr3:19188000-19189000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
41	chr3:19188000-19189000	Active TSS	A549	lung
42	chr3:19188000-19189000	Active TSS	NHDF-Ad	bronchial
43	chr3:19188000-19189200	Bivalent/Poised TSS	Primary neutrophils fromperipheralblood	blood
44	chr3:19188000-19189200	Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr3:19188000-19189200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr3:19188000-19189200	Active TSS	Stomach Mucosa	stomach
47	chr3:19188000-19189200	Active TSS	HSMM	muscle
48	chr3:19188000-19189200	Active TSS	Osteobl	bone
49	chr3:19188000-19189400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr3:19188000-19189400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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