Variant report

Variant	rs12001863
Chromosome Location	chr9:71744803-71744804
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:71649857..71652024-chr9:71744170..71747063,2	MCF-7	breast:
2	chr9:71733940..71739343-chr9:71741877..71748941,25	MCF-7	breast:
3	chr9:71743521..71745547-chr9:71821447..71823888,2	MCF-7	breast:
4	chr9:71743905..71746446-chr9:71805495..71808231,2	MCF-7	breast:
5	chr9:71734182..71738595-chr9:71741906..71745315,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119139	Chromatin interaction
ENSG00000165060	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11999809	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12000900	1.00[AMR][1000 genomes]
rs12001142	1.00[AMR][1000 genomes]
rs12001188	1.00[AMR][1000 genomes]
rs12001394	1.00[AMR][1000 genomes]
rs12001706	1.00[AMR][1000 genomes]
rs12001842	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12005295	1.00[AMR][1000 genomes]
rs17062723	1.00[AMR][1000 genomes]
rs35464930	1.00[AMR][1000 genomes]
rs35797487	1.00[AMR][1000 genomes]
rs4278214	1.00[AMR][1000 genomes]
rs60733257	1.00[AMR][1000 genomes]
rs61056981	1.00[AMR][1000 genomes]
rs7027812	1.00[AMR][1000 genomes]
rs73447162	1.00[AMR][1000 genomes]
rs73647077	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73647078	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73647079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73647080	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73647081	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73647082	0.83[AFR][1000 genomes]
rs73647083	1.00[AMR][1000 genomes]
rs73647084	1.00[AMR][1000 genomes]
rs73647085	1.00[AMR][1000 genomes]
rs73647086	1.00[AMR][1000 genomes]
rs73647087	1.00[AMR][1000 genomes]
rs73647088	1.00[AMR][1000 genomes]
rs73647089	1.00[AMR][1000 genomes]
rs73647090	1.00[AMR][1000 genomes]
rs73647092	1.00[AMR][1000 genomes]
rs73647098	1.00[AMR][1000 genomes]
rs73647099	1.00[AMR][1000 genomes]
rs73647100	1.00[AMR][1000 genomes]
rs73649624	1.00[AMR][1000 genomes]
rs73649625	1.00[AMR][1000 genomes]
rs7864925	1.00[AMR][1000 genomes]
rs7872016	1.00[AMR][1000 genomes]
rs9785300	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:33 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1053402	chr9:71399722-71819949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv540146	chr9:71399722-71819949	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv1043689	chr9:71399922-71800338	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv540147	chr9:71399922-71800338	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv1047540	chr9:71401918-71803639	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv931684	chr9:71417110-71957723	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv1049175	chr9:71418242-71986910	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv1035823	chr9:71465139-71901672	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv466396	chr9:71471912-71935577	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv614548	chr9:71471912-71935577	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
12	nsv1051798	chr9:71511805-71792032	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
13	nsv1035477	chr9:71511927-71959487	Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
14	nsv466397	chr9:71574757-71843023	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
15	nsv614550	chr9:71574757-71843023	Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
16	nsv1050692	chr9:71578494-71843023	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	nsv893416	chr9:71597840-71888601	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
18	nsv1040539	chr9:71600042-71844108	Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
19	nsv540149	chr9:71600042-71844108	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
20	nsv949664	chr9:71607398-71842391	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer 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	20 gene(s)	inside rSNPs	diseases
21	nsv948708	chr9:71632265-71842391	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
22	nsv1037787	chr9:71635338-71807648	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
23	nsv540151	chr9:71635338-71807648	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
24	nsv817209	chr9:71675454-71829412	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
25	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
26	nsv508550	chr9:71679166-71809433	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
27	nsv6550	chr9:71714144-71760048	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
28	esv1798602	chr9:71718195-71764191	Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
29	esv3398013	chr9:71722447-71746627	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
30	esv3427257	chr9:71725447-71746948	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
31	nsv511419	chr9:71733603-71746253	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
32	esv3481646	chr9:71736132-71745230	Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
33	esv1824472	chr9:71741320-71747395	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71729800-71745600	Weak transcription	K562	blood
2	chr9:71737800-71745400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr9:71738000-71745200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr9:71738000-71745200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr9:71738000-71745600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr9:71738000-71745800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr9:71738000-71745800	Weak transcription	Spleen	Spleen
8	chr9:71738000-71747000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr9:71738000-71778200	Weak transcription	Primary T cells from cord blood	blood
10	chr9:71738200-71745200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr9:71738200-71745200	Weak transcription	Fetal Kidney	kidney
12	chr9:71738200-71745400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr9:71738200-71745400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr9:71738200-71745400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr9:71738200-71745400	Weak transcription	Pancreas	Pancrea
16	chr9:71738200-71746000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr9:71738200-71748800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr9:71738200-71752400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr9:71738200-71757000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr9:71738200-71770600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr9:71738400-71745200	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr9:71738600-71745000	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr9:71738600-71745000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr9:71738600-71745400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr9:71741800-71745200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr9:71743200-71747400	Enhancers	HUVEC	blood vessel
27	chr9:71743400-71747000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr9:71743600-71745400	Enhancers	H1 Cell Line	embryonic stem cell
29	chr9:71743600-71752800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr9:71743800-71745000	Weak transcription	HMEC	breast
31	chr9:71743800-71746600	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr9:71744000-71745000	Weak transcription	Fetal Heart	heart
33	chr9:71744000-71745200	Enhancers	HepG2	liver
34	chr9:71744000-71745400	Genic enhancers	Fetal Intestine Small	intestine
35	chr9:71744000-71745600	Weak transcription	NHEK	skin
36	chr9:71744000-71746200	Weak transcription	Placenta	Placenta
37	chr9:71744000-71748400	Enhancers	Aorta	Aorta
38	chr9:71744200-71745000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr9:71744200-71745000	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr9:71744200-71745400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr9:71744200-71745400	Weak transcription	Colonic Mucosa	Colon
42	chr9:71744200-71745400	Weak transcription	Hela-S3	cervix
43	chr9:71744200-71746200	Weak transcription	Brain Angular Gyrus	brain
44	chr9:71744200-71747200	Enhancers	Lung	lung
45	chr9:71744200-71747800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr9:71744200-71749000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr9:71744400-71745000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr9:71744400-71745200	Weak transcription	Left Ventricle	heart
49	chr9:71744400-71745200	Weak transcription	Right Ventricle	heart
50	chr9:71744400-71745400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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