Variant report

Variant	rs9659680
Chromosome Location	chr1:246036766-246036767
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:246033349..246034863-chr1:246036560..246039521,2	MCF-7	breast:
2	chr1:246036446..246036946-chr3:119813818..119814549,2	Hela-S3	cervix:
3	chr1:246035292..246038297-chr1:246038719..246042153,3	MCF-7	breast:
4	chr1:246028187..246030314-chr1:246034757..246036995,2	K562	blood:
5	chr1:246035195..246037363-chr1:246059907..246062133,2	K562	blood:

Variant related genes	Relation type
ENSG00000242622	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10754483	1.00[EUR][1000 genomes]
rs10802290	1.00[EUR][1000 genomes]
rs10802291	1.00[EUR][1000 genomes]
rs10924386	1.00[EUR][1000 genomes]
rs12065652	1.00[EUR][1000 genomes]
rs2362254	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:31 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007728	chr1:245235174-246156455	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv497871	chr1:245706209-246655353	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv534412	chr1:245747724-246655416	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer 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	16 gene(s)	inside rSNPs	diseases
4	nsv1003594	chr1:245801793-246649329	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1004412	chr1:245830921-246169054	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv535385	chr1:245830921-246169054	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1011255	chr1:245913512-246065050	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv998801	chr1:245924108-246131115	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv535386	chr1:245924108-246131115	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1014841	chr1:245936464-246143222	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv535387	chr1:245936464-246143222	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv1008786	chr1:245948622-246514454	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv535388	chr1:245948622-246514454	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv468805	chr1:245950642-246229245	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv549521	chr1:245950642-246229245	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv1004119	chr1:245957145-246813150	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
17	nsv535389	chr1:245957145-246813150	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
18	nsv1014529	chr1:245957145-246817877	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
19	nsv873405	chr1:245959911-246093644	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	nsv1000654	chr1:245966390-246778182	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
21	nsv535392	chr1:245966390-246778182	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
22	nsv868852	chr1:245969229-246811220	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
23	nsv873406	chr1:245991027-246039231	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
24	nsv1005074	chr1:245999762-246141613	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
25	nsv1013699	chr1:246005308-246143361	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
26	nsv535393	chr1:246005308-246143361	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
27	nsv1003768	chr1:246024121-246169054	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
28	esv2756893	chr1:246028579-246116002	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
29	esv2759011	chr1:246028579-246116002	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
30	esv1818474	chr1:246029062-246037292	Enhancers Weak transcription Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
31	nsv441746	chr1:246029062-246037292	Weak transcription Enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:245991000-246045000	Weak transcription	Spleen	Spleen
2	chr1:245999800-246038400	Weak transcription	Aorta	Aorta
3	chr1:246001800-246056800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:246006800-246041200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:246009600-246038200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr1:246012800-246049600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:246015400-246038200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr1:246019200-246067400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr1:246021000-246038200	Weak transcription	Pancreas	Pancrea
10	chr1:246022000-246037800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:246022000-246038200	Weak transcription	Gastric	stomach
12	chr1:246022000-246042600	Weak transcription	Fetal Intestine Small	intestine
13	chr1:246022200-246037800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:246023000-246038200	Weak transcription	Fetal Kidney	kidney
15	chr1:246023600-246037000	Weak transcription	Lung	lung
16	chr1:246023600-246038200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:246023600-246038400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:246024400-246038200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr1:246024800-246037400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr1:246024800-246037800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr1:246025000-246037000	Weak transcription	Left Ventricle	heart
22	chr1:246025400-246037800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:246027000-246037800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:246027200-246037600	Weak transcription	Primary B cells from peripheral blood	blood
25	chr1:246027200-246041600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr1:246029600-246038200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr1:246030600-246037400	Enhancers	Fetal Heart	heart
28	chr1:246033200-246037600	Strong transcription	K562	blood
29	chr1:246033800-246038000	Weak transcription	Placenta	Placenta
30	chr1:246033800-246038200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:246033800-246039600	Enhancers	NHDF-Ad	bronchial
32	chr1:246034000-246038000	Enhancers	NH-A	brain
33	chr1:246034600-246038000	Enhancers	NHLF	lung
34	chr1:246034600-246039800	Enhancers	Osteobl	bone
35	chr1:246034800-246036800	Strong transcription	Primary T cells from cord blood	blood
36	chr1:246034800-246045600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:246035000-246037200	Weak transcription	Brain Germinal Matrix	brain
38	chr1:246035200-246037800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr1:246035200-246038000	Weak transcription	HSMM	muscle
40	chr1:246035400-246038000	Weak transcription	Right Atrium	heart
41	chr1:246035400-246038200	Enhancers	Colon Smooth Muscle	Colon
42	chr1:246035400-246041600	Enhancers	Placenta Amnion	Placenta Amnion
43	chr1:246035600-246036800	Weak transcription	Fetal Lung	lung
44	chr1:246035600-246037400	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr1:246035600-246038000	Enhancers	Stomach Smooth Muscle	stomach
46	chr1:246035600-246038200	Weak transcription	Psoas Muscle	Psoas
47	chr1:246035600-246041600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr1:246035600-246042200	Weak transcription	HepG2	liver
49	chr1:246035800-246038000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:246035800-246038200	Weak transcription	Fetal Muscle Trunk	muscle

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