Variant report

Variant	rs955216
Chromosome Location	chr3:141029860-141029861
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:60)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:60 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:141029730-141030085	U87	brain:	n/a	n/a
2	POLR2A	chr3:141029848-141031086	GM18526	blood:	n/a	n/a
3	GATA1	chr3:141029608-141033138	K562	blood:	n/a	chr3:141031684-141031693 chr3:141031986-141031996 chr3:141031704-141031714 chr3:141031706-141031723 chr3:141031705-141031714 chr3:141031747-141031755 chr3:141031684-141031691 chr3:141031683-141031693
4	GABPA	chr3:141029843-141031331	MCF-7	breast:	n/a	chr3:141030693-141030700
5	POLR2A	chr3:141029682-141031738	GM12892	blood:	n/a	n/a
6	POLR2A	chr3:141029448-141031315	PFSK-1	brain:	n/a	n/a
7	ELF1	chr3:141029841-141031076	GM12878	blood:	n/a	n/a
8	POLR2A	chr3:141029165-141031551	GM12891	blood:	n/a	n/a
9	E2F6	chr3:141029735-141031099	K562	blood:	n/a	chr3:141030530-141030541 chr3:141030359-141030366
10	POLR2A	chr3:141029384-141031221	K562	blood:	n/a	n/a
11	POLR2A	chr3:141029345-141031366	GM19193	blood:	n/a	n/a
12	POLR2A	chr3:141029238-141032588	K562	blood:	n/a	n/a
13	MAX	chr3:141029834-141031394	A549	lung:	n/a	n/a
14	POLR2A	chr3:141029331-141029866	HepG2	liver:	n/a	n/a
15	HCFC1	chr3:141029652-141031281	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr3:141029200-141031801	GM12878	blood:	n/a	n/a
17	POLR2A	chr3:141029466-141031119	Raji	blood:	n/a	n/a
18	POLR2A	chr3:141029759-141032733	PBDE	blood:	n/a	n/a
19	POLR2A	chr3:141029839-141031064	ECC-1	luminal epithelium:	n/a	n/a
20	TCF12	chr3:141029839-141031259	A549	lung:	n/a	n/a
21	MXI1	chr3:141029799-141031576	IMR90	lung:	n/a	n/a
22	POLR2A	chr3:141029101-141030108	K562	blood:	n/a	n/a
23	POLR2A	chr3:141029463-141031649	GM12878	blood:	n/a	n/a
24	POLR2A	chr3:141029587-141031135	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr3:141029579-141031228	K562	blood:	n/a	n/a
26	PML	chr3:141029300-141031233	GM12878	blood:	n/a	chr3:141030794-141030802
27	POLR2A	chr3:141029628-141031255	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr3:141029674-141031012	K562	blood:	n/a	n/a
29	POLR2A	chr3:141029806-141031129	HL-60	blood:	n/a	n/a
30	POLR2A	chr3:141029621-141029866	MCF-7	breast:	n/a	n/a
31	CREB1	chr3:141029841-141030951	K562	blood:	n/a	n/a
32	BHLHE40	chr3:141029670-141029923	K562	blood:	n/a	n/a
33	POLR2A	chr3:141029450-141030937	U87	brain:	n/a	n/a
34	MYC	chr3:141029760-141031148	K562	blood:	n/a	n/a
35	POLR2A	chr3:141029791-141032645	K562	blood:	n/a	n/a
36	POLR2A	chr3:141029341-141030995	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr3:141029220-141031079	HepG2	liver:	n/a	n/a
38	USF2	chr3:141029526-141029987	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr3:141029536-141031194	GM12892	blood:	n/a	n/a
40	POLR2A	chr3:141029574-141031075	PFSK-1	brain:	n/a	n/a
41	POLR2A	chr3:141029704-141031064	HEK293	kidney:	n/a	n/a
42	MTA3	chr3:141029608-141031699	GM12878	blood:	n/a	n/a
43	POLR2A	chr3:141029601-141029951	HepG2	liver:	n/a	n/a
44	HEY1	chr3:141029636-141031106	K562	blood:	n/a	n/a
45	POLR2A	chr3:141028900-141031231	SK-N-MC	brain:	n/a	n/a
46	POLR2A	chr3:141029712-141031542	GM18505	blood:	n/a	n/a
47	MXI1	chr3:141029544-141031434	SK-N-SH	brain:	n/a	n/a
48	POLR2A	chr3:141029636-141031356	GM19099	blood:	n/a	n/a
49	POLR2A	chr3:141029687-141031105	K562	blood:	n/a	n/a
50	POLR2A	chr3:141029857-141031250	GM12892	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:141029221..141032005-chr3:141199464..141200982,2	MCF-7	breast:
2	chr17:57920552..57922129-chr3:141029319..141031208,2	MCF-7	breast:
3	chr3:141021371..141023874-chr3:141028085..141030183,2	K562	blood:
4	chr3:141029860..141032097-chr3:141173989..141175746,3	K562	blood:
5	chr3:141028495..141032567-chr3:141157435..141162053,7	K562	blood:
6	chr3:140950249..140951889-chr3:141027537..141030239,2	MCF-7	breast:
7	chr3:141029007..141031829-chr3:141128539..141131843,4	MCF-7	breast:
8	chr3:140946468..140949037-chr3:141029081..141031629,2	MCF-7	breast:
9	chr3:141028766..141032567-chr3:141157435..141160159,4	K562	blood:
10	chr3:141020173..141025458-chr3:141027736..141031856,6	K562	blood:
11	chr3:141028943..141030664-chr3:141287005..141289345,2	MCF-7	breast:
12	chr3:141023312..141027474-chr3:141027786..141032081,5	MCF-7	breast:
13	chr3:141029632..141032040-chr3:141170273..141172073,2	K562	blood:
14	chr3:140998105..140999651-chr3:141029649..141032061,2	K562	blood:
15	chr3:141027145..141033256-chr3:141085204..141089995,12	K562	blood:
16	chr3:141029377..141033531-chr3:141165560..141167342,4	MCF-7	breast:
17	chr3:141028623..141032743-chr3:141076399..141079995,4	K562	blood:
18	chr3:141029410..141031621-chr3:141132926..141134468,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TFDP2-11	chr3:141025328-141030534	NONHSAT092424

No data

Variant related genes	Relation type
ENSG00000249540	TF binding region
ENSG00000249540	Chromatin interaction
ENSG00000177311	Chromatin interaction
ENSG00000155893	Chromatin interaction
ENSG00000249417	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11927391	0.82[AMR][1000 genomes]
rs12630390	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[EUR][1000 genomes]
rs6439997	0.92[ASN][1000 genomes]
rs6773133	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[EUR][1000 genomes]
rs9968231	0.88[CHB][hapmap];0.90[GIH][hapmap];0.86[MEX][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	nsv877551	chr3:140970556-141029860	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv829744	chr3:141016749-141189168	Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv460871	chr3:141027614-141074962	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv591893	chr3:141027614-141074962	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141014000-141030000	Weak transcription	Aorta	Aorta
2	chr3:141022800-141030000	Weak transcription	HSMMtube	muscle
3	chr3:141023000-141030000	Weak transcription	Esophagus	oesophagus
4	chr3:141027200-141030000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr3:141028000-141030000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:141029200-141030000	Flanking Active TSS	GM12878-XiMat	blood
7	chr3:141029400-141030000	Flanking Active TSS	K562	blood
8	chr3:141029400-141030200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr3:141029400-141030400	Flanking Active TSS	Dnd41	blood
10	chr3:141029400-141031000	Active TSS	A549	lung
11	chr3:141029600-141030000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
12	chr3:141029600-141030000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:141029600-141030000	Enhancers	Colonic Mucosa	Colon
14	chr3:141029600-141030000	Enhancers	Fetal Heart	heart
15	chr3:141029600-141030000	Enhancers	Gastric	stomach
16	chr3:141029600-141030000	Enhancers	Pancreas	Pancrea
17	chr3:141029600-141030000	Flanking Active TSS	HepG2	liver
18	chr3:141029600-141030200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:141029600-141030200	Flanking Active TSS	Liver	Liver
20	chr3:141029600-141030200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
21	chr3:141029600-141030200	Flanking Active TSS	Hela-S3	cervix
22	chr3:141029600-141030400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:141029600-141030400	Flanking Active TSS	Primary T cells from cord blood	blood
24	chr3:141029600-141030400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:141029600-141030400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:141029600-141030800	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr3:141029600-141030800	Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr3:141029600-141031000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:141029600-141031000	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr3:141029600-141031000	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr3:141029600-141031000	Active TSS	Rectal Smooth Muscle	rectum
32	chr3:141029600-141031200	Active TSS	H9 Cell Line	embryonic stem cell
33	chr3:141029600-141031600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr3:141029600-141031600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr3:141029800-141030000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
36	chr3:141029800-141030000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:141029800-141030000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:141029800-141030000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:141029800-141030000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
40	chr3:141029800-141030000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:141029800-141030000	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr3:141029800-141030000	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr3:141029800-141030000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr3:141029800-141030000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr3:141029800-141030000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:141029800-141030000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr3:141029800-141030000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr3:141029800-141030000	Active TSS	Fetal Muscle Trunk	muscle
49	chr3:141029800-141030000	Enhancers	Fetal Muscle Leg	muscle
50	chr3:141029800-141030000	Enhancers	Placenta	Placenta

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