Variant report

Variant	rs6725867
Chromosome Location	chr2:96874590-96874591
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	CTCF	chr2:96874440-96874590	GM12874	blood:	n/a	n/a
2	POLR2A	chr2:96873860-96874699	A549	lung:	n/a	n/a
3	TAF1	chr2:96873765-96874988	GM12878	blood:	n/a	n/a
4	POLR2A	chr2:96873661-96874981	HepG2	liver:	n/a	n/a
5	TAL1	chr2:96873010-96875135	K562	blood:	n/a	n/a
6	STAT5A	chr2:96874368-96874702	GM12878	blood:	n/a	n/a
7	NR2F2	chr2:96874377-96874852	K562	blood:	n/a	n/a
8	ZBTB33	chr2:96874519-96874904	HCT-116	colon:	n/a	n/a
9	TAF7	chr2:96873865-96874959	H1-hESC	embryonic stem cell:	n/a	n/a
10	SIN3AK20	chr2:96873796-96874856	K562	blood:	n/a	n/a
11	POLR2A	chr2:96872978-96875681	PBDE	blood:	n/a	n/a
12	RFX5	chr2:96874543-96874706	K562	blood:	n/a	n/a
13	NFYA	chr2:96874485-96874878	GM12878	blood:	n/a	chr2:96874634-96874652
14	NFIC	chr2:96873871-96874935	HepG2	liver:	n/a	n/a
15	YY1	chr2:96874026-96874988	K562	blood:	n/a	chr2:96874789-96874811 chr2:96874789-96874799 chr2:96874773-96874784 chr2:96874921-96874930 chr2:96874787-96874806 chr2:96874948-96874959 chr2:96874790-96874798
16	EP300	chr2:96873724-96875048	SK-N-SH	brain:	n/a	chr2:96874809-96874825
17	SP1	chr2:96873834-96874971	A549	lung:	n/a	chr2:96874920-96874932 chr2:96874811-96874823 chr2:96874812-96874821 chr2:96874921-96874931 chr2:96874813-96874822 chr2:96874664-96874675 chr2:96874921-96874931 chr2:96874922-96874931 chr2:96874921-96874930 chr2:96874922-96874931 chr2:96874920-96874932 chr2:96874811-96874823 chr2:96874917-96874931 chr2:96874812-96874821
18	MAFF	chr2:96874522-96874736	HepG2	liver:	n/a	n/a
19	ESRRA	chr2:96873846-96874902	HepG2	liver:	n/a	n/a
20	POLR2A	chr2:96873523-96875035	GM12892	blood:	n/a	n/a
21	POLR2A	chr2:96873791-96874959	MCF-7	breast:	n/a	n/a
22	ELK1	chr2:96873129-96874895	GM12878	blood:	n/a	n/a
23	GATA3	chr2:96874333-96874986	MCF-7	breast:	n/a	n/a
24	ARID3A	chr2:96873643-96875094	HepG2	liver:	n/a	n/a
25	POLR2A	chr2:96873750-96874967	SK-N-SH	brain:	n/a	n/a
26	CTCF	chr2:96874520-96874670	HCFaa	heart:	n/a	n/a
27	CTCF	chr2:96874520-96874670	HFF-Myc	foreskin:	n/a	n/a
28	POLR2A	chr2:96873598-96874981	PFSK-1	brain:	n/a	n/a
29	TAF1	chr2:96873804-96875022	H1-neurons	neurons:	n/a	n/a
30	GATA3	chr2:96873574-96874927	A549	lung:	n/a	n/a
31	TAF1	chr2:96873734-96874885	HepG2	liver:	n/a	n/a
32	RAD21	chr2:96873917-96874678	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr2:96873673-96875043	K562	blood:	n/a	n/a
34	MXI1	chr2:96872609-96875419	SK-N-SH	brain:	n/a	n/a
35	TBP	chr2:96873473-96874854	GM12878	blood:	n/a	n/a
36	CREB1	chr2:96874452-96874752	A549	lung:	n/a	n/a
37	MAFK	chr2:96874342-96874785	HepG2	liver:	n/a	n/a
38	YY1	chr2:96873745-96875027	GM12892	blood:	n/a	chr2:96874789-96874811 chr2:96874789-96874799 chr2:96874773-96874784 chr2:96874921-96874930 chr2:96874787-96874806 chr2:96874948-96874959 chr2:96874790-96874798
39	STAT3	chr2:96874507-96874953	MCF10A-Er-Src	breast:	n/a	chr2:96874808-96874820
40	NRF1	chr2:96873880-96874959	Hela-S3	cervix:	n/a	chr2:96874064-96874075 chr2:96874921-96874930
41	MYC	chr2:96874516-96874628	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr2:96873247-96875061	PANC-1	pancreas:	n/a	n/a
43	GTF2B	chr2:96874407-96874767	K562	blood:	n/a	n/a
44	TEAD4	chr2:96874353-96874968	K562	blood:	n/a	n/a
45	ELF1	chr2:96873953-96874900	HepG2	liver:	n/a	n/a
46	POLR2A	chr2:96872641-96874903	HepG2	liver:	n/a	n/a
47	TAF1	chr2:96873819-96874801	GM12891	blood:	n/a	n/a
48	EGR1	chr2:96873884-96874959	HCT-116	colon:	n/a	chr2:96874919-96874929 chr2:96874916-96874929 chr2:96874921-96874931 chr2:96874664-96874678
49	MAX	chr2:96874455-96874927	H1-hESC	embryonic stem cell:	n/a	n/a
50	ZBTB33	chr2:96874323-96874650	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:96874070..96874653-chr3:156877633..156878329,3	Hela-S3	cervix:
2	chr2:96872884..96875870-chr2:96999913..97003204,4	MCF-7	breast:
3	chr11:62609137..62610090-chr2:96874054..96874684,2	Hela-S3	cervix:
4	chr2:96873368..96875940-chr2:96925082..96928161,5	MCF-7	breast:
5	chr10:22605078..22605639-chr2:96874020..96874816,2	HCT-116	colon:
6	chr13:24734748..24735310-chr2:96874094..96874602,2	Hela-S3	cervix:
7	chr2:96874147..96874759-chr6:26033236..26033940,2	Hela-S3	cervix:
8	chr2:96656872..96660081-chr2:96874473..96876452,3	MCF-7	breast:
9	chr2:96872598..96876007-chr2:96924059..96928423,13	MCF-7	breast:
10	chr2:96873130..96877842-chr2:96924423..96928437,5	K562	blood:
11	chr2:96678269..96680437-chr2:96873411..96875898,2	MCF-7	breast:
12	chr2:96856180..96863246-chr2:96870668..96875373,10	MCF-7	breast:
13	chr2:96802498..96805773-chr2:96872667..96874693,3	MCF-7	breast:
14	chr2:96808076..96814305-chr2:96871431..96875215,8	MCF-7	breast:
15	chr2:96872287..96875218-chr2:97169522..97172410,2	MCF-7	breast:
16	chr1:201951655..201952284-chr2:96873670..96874594,2	HCT-116	colon:
17	chr12:7071203..7073201-chr2:96873303..96874829,2	MCF-7	breast:
18	chr2:96808739..96811929-chr2:96872960..96875920,3	MCF-7	breast:
19	chr2:96868913..96876440-chr2:96928017..96934530,23	K562	blood:
20	chr2:96870309..96876262-chr2:96928720..96933891,16	MCF-7	breast:
21	chr2:96803968..96806803-chr2:96872820..96874681,2	K562	blood:
22	chr2:96873882..96874865-chr22:41842441..41843336,2	HCT-116	colon:
23	chr2:96871739..96877156-chr2:96928674..96935050,17	K562	blood:
24	chr2:96874014..96875585-chr2:96990690..96992909,2	K562	blood:
25	chr2:96871572..96876906-chr2:96928916..96935631,15	MCF-7	breast:
26	chr2:96801466..96803641-chr2:96873708..96877456,3	MCF-7	breast:
27	chr2:96874408..96876271-chr2:96925161..96927177,2	K562	blood:
28	chr2:96873349..96876341-chr2:97001503..97003498,3	K562	blood:
29	chr2:96873776..96875796-chr2:96905403..96907728,3	MCF-7	breast:
30	chr2:96873119..96874915-chr2:97202040..97204570,2	K562	blood:
31	chr12:49658650..49659484-chr2:96874043..96874610,3	Hela-S3	cervix:
32	chr2:96872802..96875592-chr2:97201053..97203640,2	K562	blood:
33	chr17:57913629..57916404-chr2:96873395..96876100,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CIAO1-1	chr2:96874154-96874717	ENSG00000204685.5
2	lnc-CIAO1-1	chr2:96874154-96874717	NONHSAT072550

Variant related genes	Relation type
STARD7	TF binding region
ENSG00000182957	Chromatin interaction
ENSG00000204685	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000163660	Chromatin interaction
ENSG00000158050	Chromatin interaction
ENSG00000196843	Chromatin interaction
ENSG00000207713	Chromatin interaction
ENSG00000144021	Chromatin interaction
ENSG00000257084	Chromatin interaction
ENSG00000163121	Chromatin interaction
ENSG00000174501	Chromatin interaction
ENSG00000084090	Chromatin interaction
ENSG00000126749	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000269897	Chromatin interaction
ENSG00000183864	Chromatin interaction
ENSG00000231584	Chromatin interaction
ENSG00000137259	Chromatin interaction
ENSG00000228873	Chromatin interaction
ENSG00000135956	Chromatin interaction
ENSG00000188886	Chromatin interaction
ENSG00000198885	Chromatin interaction
ENSG00000176393	Chromatin interaction
ENSG00000121152	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000148444	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11551400	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11886999	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2016759	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57251156	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61697794	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6725872	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7579553	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS 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 miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	esv3435047	chr2:96836850-96890437	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv834305	chr2:96848898-97019476	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
9	nsv874679	chr2:96860971-97184160	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96870000-96875400	Active TSS	Psoas Muscle	Psoas
2	chr2:96870400-96875400	Active TSS	Right Ventricle	heart
3	chr2:96871400-96875200	Active TSS	Left Ventricle	heart
4	chr2:96871400-96875400	Active TSS	NHLF	lung
5	chr2:96871600-96875200	Active TSS	Aorta	Aorta
6	chr2:96872200-96875000	Active TSS	GM12878-XiMat	blood
7	chr2:96872200-96875200	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr2:96872200-96875200	Active TSS	Fetal Intestine Large	intestine
9	chr2:96872200-96875200	Active TSS	HSMMtube	muscle
10	chr2:96872600-96874600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr2:96872600-96875400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr2:96872800-96874600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
13	chr2:96872800-96875200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr2:96872800-96875200	Active TSS	Brain Substantia Nigra	brain
15	chr2:96872800-96875200	Active TSS	Fetal Intestine Small	intestine
16	chr2:96872800-96875200	Active TSS	Fetal Muscle Trunk	muscle
17	chr2:96872800-96875200	Active TSS	Lung	lung
18	chr2:96872800-96875200	Active TSS	Ovary	ovary
19	chr2:96873000-96874600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
20	chr2:96873000-96875000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:96873000-96875000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr2:96873000-96875000	Active TSS	Esophagus	oesophagus
23	chr2:96873000-96875200	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr2:96873000-96875200	Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr2:96873000-96875200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr2:96873000-96875200	Active TSS	Pancreas	Pancrea
27	chr2:96873000-96875400	Active TSS	H1 Cell Line	embryonic stem cell
28	chr2:96873000-96875600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:96873200-96875000	Active TSS	Brain Anterior Caudate	brain
30	chr2:96873200-96875000	Active TSS	Gastric	stomach
31	chr2:96873200-96875000	Active TSS	Sigmoid Colon	Sigmoid Colon
32	chr2:96873200-96875000	Active TSS	Small Intestine	intestine
33	chr2:96873200-96875000	Active TSS	Stomach Mucosa	stomach
34	chr2:96873200-96875200	Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr2:96873200-96875200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:96873200-96875200	Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr2:96873200-96875200	Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr2:96873200-96875200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr2:96873200-96875200	Active TSS	Muscle Satellite Cultured Cells	--
40	chr2:96873200-96875200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr2:96873200-96875200	Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr2:96873200-96875200	Active TSS	Fetal Kidney	kidney
43	chr2:96873200-96875200	Active TSS	Placenta Amnion	Placenta Amnion
44	chr2:96873200-96875400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:96873200-96875400	Active TSS	A549	lung
46	chr2:96873200-96875400	Active TSS	NHDF-Ad	bronchial
47	chr2:96873400-96875000	Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr2:96873400-96875000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr2:96873400-96875000	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr2:96873400-96875000	Active TSS	Thymus	Thymus

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