Variant report

Variant	rs11921543
Chromosome Location	chr3:196015344-196015345
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:46)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:46 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GABPA	chr3:196013990-196015363	A549	lung:	n/a	n/a
2	POLR2A	chr3:196014121-196015468	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr3:196013746-196016683	SK-N-MC	brain:	n/a	n/a
4	TEAD4	chr3:196013769-196015351	K562	blood:	n/a	n/a
5	MAZ	chr3:196013703-196015449	IMR90	lung:	n/a	chr3:196014268-196014278
6	NFIC	chr3:196014151-196015384	GM12878	blood:	n/a	n/a
7	TAF1	chr3:196014013-196015351	MCF-7	breast:	n/a	n/a
8	MAX	chr3:196013964-196015474	A549	lung:	n/a	chr3:196014268-196014278
9	REST	chr3:196013834-196015425	H1-neurons	neurons:	n/a	chr3:196014757-196014770 chr3:196014969-196014979
10	POLR2A	chr3:196013879-196015732	MCF-7	breast:	n/a	n/a
11	POLR2A	chr3:196014163-196015405	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr3:196013987-196015736	MCF-7	breast:	n/a	n/a
13	MXI1	chr3:196013686-196016157	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr3:196013921-196015406	HepG2	liver:	n/a	n/a
15	USF1	chr3:196013846-196015354	ECC-1	luminal epithelium:	n/a	chr3:196015019-196015035 chr3:196015027-196015043
16	CBX3	chr3:196013928-196015353	K562	blood:	n/a	n/a
17	POLR2A	chr3:196014280-196015374	U87	brain:	n/a	n/a
18	CREB1	chr3:196013883-196015344	HepG2	liver:	n/a	n/a
19	HCFC1	chr3:196013764-196015394	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr3:196014299-196015400	MCF10A-Er-Src	breast:	n/a	n/a
21	EP300	chr3:196013864-196015359	ECC-1	luminal epithelium:	n/a	chr3:196014121-196014137 chr3:196014967-196014983
22	POLR2A	chr3:196014264-196015364	K562	blood:	n/a	n/a
23	POLR2A	chr3:196013997-196015795	K562	blood:	n/a	n/a
24	MYC	chr3:196014038-196015350	K562	blood:	n/a	chr3:196014268-196014278
25	MAX	chr3:196013835-196015500	ECC-1	luminal epithelium:	n/a	chr3:196014268-196014278
26	MAX	chr3:196013781-196015471	ECC-1	luminal epithelium:	n/a	chr3:196014268-196014278
27	POLR2A	chr3:196014260-196015374	U87	brain:	n/a	n/a
28	MTA3	chr3:196013760-196015383	GM12878	blood:	n/a	n/a
29	GABPA	chr3:196013916-196015375	MCF-7	breast:	n/a	n/a
30	POLR2A	chr3:196014047-196015860	PANC-1	pancreas:	n/a	n/a
31	FOXM1	chr3:196014190-196015387	GM12878	blood:	n/a	n/a
32	ATF2	chr3:196014248-196015394	GM12878	blood:	n/a	chr3:196014532-196014546
33	MXI1	chr3:196013781-196015538	IMR90	lung:	n/a	n/a
34	MAX	chr3:196014006-196015450	MCF-7	breast:	n/a	chr3:196014268-196014278
35	MAX	chr3:196013815-196015406	MCF-7	breast:	n/a	chr3:196014268-196014278
36	POLR2A	chr3:196014140-196015419	HUVEC	blood vessel:	n/a	n/a
37	MYC	chr3:196014470-196015364	MCF10A-Er-Src	breast:	n/a	n/a
38	MAX	chr3:196013963-196015379	NB4	blood:	n/a	chr3:196014268-196014278
39	MAX	chr3:196013845-196015447	HepG2	liver:	n/a	chr3:196014268-196014278
40	POLR2A	chr3:196014231-196015648	PFSK-1	brain:	n/a	n/a
41	POLR2A	chr3:196014141-196015400	U87	brain:	n/a	n/a
42	POLR2A	chr3:196014307-196015356	SK-N-SH	brain:	n/a	n/a
43	SIN3AK20	chr3:196013758-196015541	MCF-7	breast:	n/a	n/a
44	MYC	chr3:196014459-196015373	MCF10A-Er-Src	breast:	n/a	n/a
45	GABPA	chr3:196013816-196015545	MCF-7	breast:	n/a	n/a
46	STAT5A	chr3:196013765-196015386	GM12878	blood:	n/a	n/a

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:26232203..26232954-chr3:196014915..196015415,2	Hela-S3	cervix:
2	chr3:196012776..196015922-chr3:196063347..196066816,3	MCF-7	breast:
3	chr3:196013519..196016421-chr3:196024534..196027087,2	K562	blood:
4	chr3:196012377..196016502-chr3:196041586..196047553,11	K562	blood:
5	chr3:195965458..195967733-chr3:196012588..196015404,2	MCF-7	breast:
6	chr3:196013567..196017227-chr3:196043342..196045325,4	MCF-7	breast:
7	chr3:196014537..196016415-chr3:196229117..196231929,2	MCF-7	breast:
8	chr3:196014832..196016725-chr3:196229110..196231842,2	K562	blood:
9	chr3:196013815..196016163-chr6:27090213..27092532,2	MCF-7	breast:
10	chr3:196015046..196017473-chr3:196021246..196023038,2	K562	blood:
11	chr3:196014705..196016276-chr3:196018024..196020194,2	K562	blood:
12	chr3:196014550..196016725-chr3:196229110..196232092,4	K562	blood:
13	chr3:196012352..196016755-chr3:196062622..196069148,9	K562	blood:
14	chr3:196012576..196016636-chr3:196061383..196069148,11	K562	blood:
15	chr3:196014592..196016192-chr3:196157861..196160786,2	MCF-7	breast:
16	chr3:196013508..196016403-chr3:196043043..196046288,6	MCF-7	breast:
17	chr3:196013398..196015851-chr3:196068583..196071493,3	MCF-7	breast:
18	chr3:196014434..196017243-chr3:196157002..196159307,2	K562	blood:

No data

Variant related genes	Relation type
PCYT1A	TF binding region
ENSG00000272468	Chromatin interaction
ENSG00000273331	Chromatin interaction
ENSG00000212146	Chromatin interaction
ENSG00000237418	Chromatin interaction
ENSG00000225822	Chromatin interaction
ENSG00000264021	Chromatin interaction
ENSG00000161217	Chromatin interaction
ENSG00000272741	Chromatin interaction
ENSG00000213123	Chromatin interaction
ENSG00000163960	Chromatin interaction
ENSG00000145107	Chromatin interaction
ENSG00000235897	Chromatin interaction
ENSG00000117632	Chromatin interaction
ENSG00000163961	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11920918	1.00[AMR][1000 genomes]
rs11922994	1.00[AMR][1000 genomes]
rs11926608	1.00[AMR][1000 genomes]
rs11928172	1.00[AMR][1000 genomes]
rs34898770	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759213	chr3:195102787-196071593	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	esv2757913	chr3:195379484-196071593	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
3	nsv532213	chr3:195643944-196063636	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	nsv997797	chr3:195658360-196212958	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	nsv432543	chr3:195746690-196015690	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
6	nsv1009811	chr3:195851796-196138071	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
7	nsv461131	chr3:195858887-196072442	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
8	nsv593071	chr3:195858887-196072442	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
9	nsv1009178	chr3:195864466-196081670	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
10	nsv536892	chr3:195864466-196081670	Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Active TSS 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	51 gene(s)	inside rSNPs	diseases
11	nsv1003550	chr3:195885340-196159824	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
12	nsv536893	chr3:195885340-196159824	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
13	nsv878179	chr3:195929268-196019680	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
14	nsv1014563	chr3:195934010-196085951	Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
15	nsv878180	chr3:195946535-196066569	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
16	nsv878181	chr3:195946535-196072442	Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
17	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
18	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
19	nsv878182	chr3:195974181-196228360	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196012400-196015400	Active TSS	Rectal Smooth Muscle	rectum
2	chr3:196012400-196015600	Active TSS	HSMMtube	muscle
3	chr3:196012600-196015400	Active TSS	Colonic Mucosa	Colon
4	chr3:196012600-196015800	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr3:196012800-196015600	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr3:196013000-196015400	Active TSS	NHLF	lung
7	chr3:196013000-196015600	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr3:196013000-196015600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:196013000-196015600	Active TSS	Small Intestine	intestine
10	chr3:196013200-196015400	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr3:196013200-196015400	Active TSS	Sigmoid Colon	Sigmoid Colon
12	chr3:196013200-196015600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:196013200-196015600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:196013200-196015600	Active TSS	Fetal Intestine Small	intestine
15	chr3:196013200-196015600	Active TSS	Left Ventricle	heart
16	chr3:196013200-196015600	Active TSS	Psoas Muscle	Psoas
17	chr3:196013200-196015600	Active TSS	Right Ventricle	heart
18	chr3:196013200-196015800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:196013400-196015400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:196013400-196015400	Active TSS	Cortex derived primary cultured neurospheres	brain
21	chr3:196013400-196015400	Active TSS	HMEC	breast
22	chr3:196013400-196015400	Active TSS	NHDF-Ad	bronchial
23	chr3:196013400-196015600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:196013400-196015600	Active TSS	Muscle Satellite Cultured Cells	--
25	chr3:196013400-196015600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:196013400-196015600	Active TSS	GM12878-XiMat	blood
27	chr3:196013400-196015600	Active TSS	K562	blood
28	chr3:196013400-196015800	Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr3:196013400-196015800	Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr3:196013400-196015800	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr3:196013400-196015800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:196013400-196015800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:196013400-196015800	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr3:196013400-196015800	Active TSS	A549	lung
35	chr3:196013400-196015800	Active TSS	HSMM	muscle
36	chr3:196013400-196015800	Active TSS	NHEK	skin
37	chr3:196013400-196016000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:196013600-196015400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:196013600-196015400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr3:196013600-196015400	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr3:196013600-196015400	Active TSS	Lung	lung
42	chr3:196013600-196015600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:196013600-196015600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:196013600-196015600	Active TSS	Brain Angular Gyrus	brain
45	chr3:196013600-196015600	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr3:196013600-196015600	Active TSS	HUVEC	blood vessel
47	chr3:196013600-196015800	Active TSS	H1 Cell Line	embryonic stem cell
48	chr3:196013600-196015800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:196013600-196015800	Active TSS	Fetal Intestine Large	intestine
50	chr3:196013600-196015800	Active TSS	Stomach Smooth Muscle	stomach

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