Variant report

Variant	rs12040761
Chromosome Location	chr1:246008315-246008316
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10754479	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10924359	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12024763	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12026480	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12031535	0.83[CHB][hapmap]
rs12034110	0.83[CHB][hapmap]
rs12036285	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12038930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12040678	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs12127001	0.86[ASN][1000 genomes]
rs12407509	0.81[CHB][hapmap];0.80[EUR][1000 genomes]
rs12411183	0.80[EUR][1000 genomes]
rs1890820	0.91[ASN][1000 genomes]
rs2153405	0.87[ASN][1000 genomes]
rs2153406	0.90[ASN][1000 genomes]
rs2362926	0.83[CHB][hapmap]
rs2885549	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs34182761	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34420508	0.87[ASN][1000 genomes]
rs34677309	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35650462	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4314851	0.81[CHB][hapmap]
rs7521049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9728593	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 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	nsv1007095	chr1:245964829-246012247	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	nsv535390	chr1:245964829-246012247	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
22	nsv1001290	chr1:245966190-246018587	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
23	nsv535391	chr1:245966190-246018587	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
24	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
25	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
26	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
27	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
28	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
29	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
30	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

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:245974400-246020800	Weak transcription	Fetal Intestine Small	intestine
2	chr1:245986600-246021600	Weak transcription	Fetal Stomach	stomach
3	chr1:245986800-246014000	Weak transcription	Primary T cells from cord blood	blood
4	chr1:245987000-246015000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:245990800-246016600	Weak transcription	Lung	lung
6	chr1:245990800-246019000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr1:245991000-246018000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:245991000-246045000	Weak transcription	Spleen	Spleen
9	chr1:245991200-246019200	Weak transcription	Pancreas	Pancrea
10	chr1:245994400-246018000	Weak transcription	HepG2	liver
11	chr1:245996800-246021200	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr1:245997000-246015200	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr1:245997600-246023800	Weak transcription	Ovary	ovary
14	chr1:245998000-246020400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:245998200-246020800	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr1:245998400-246017600	Weak transcription	Primary B cells from cord blood	blood
17	chr1:245999400-246019200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:245999400-246024200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr1:245999800-246038400	Weak transcription	Aorta	Aorta
20	chr1:246000200-246008800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr1:246000200-246019200	Weak transcription	Gastric	stomach
22	chr1:246000200-246019200	Weak transcription	NHLF	lung
23	chr1:246000800-246019200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:246001200-246023400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:246001800-246015000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:246001800-246016200	Weak transcription	Osteobl	bone
27	chr1:246001800-246016600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:246001800-246019200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:246001800-246019200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:246001800-246056800	Weak transcription	Primary hematopoietic stem cells	blood
31	chr1:246006000-246012400	Weak transcription	HUVEC	blood vessel
32	chr1:246006600-246011600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:246006600-246021800	Weak transcription	Fetal Muscle Leg	muscle
34	chr1:246006800-246041200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:246007000-246010600	Strong transcription	K562	blood
36	chr1:246007000-246019200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr1:246007200-246015000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:246007600-246019600	Weak transcription	Brain Hippocampus Middle	brain
39	chr1:246007800-246019400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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