Variant report

Variant	rs4654123
Chromosome Location	chr1:246799729-246799730
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	POLR2A	chr1:246799129-246799920	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000228955	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10754528	0.84[ASN][1000 genomes]
rs10754530	0.89[ASN][1000 genomes]
rs10924785	0.89[ASN][1000 genomes]
rs3006082	0.85[ASN][1000 genomes]
rs3006085	0.89[ASN][1000 genomes]
rs3007401	0.85[ASN][1000 genomes]
rs3007405	0.84[ASN][1000 genomes]
rs3007406	0.89[ASN][1000 genomes]
rs3124075	0.88[ASN][1000 genomes]
rs3124077	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3124078	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3124079	0.94[ASN][1000 genomes]
rs3124084	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3129542	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3129544	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3129546	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3129547	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3129549	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3129552	0.89[ASN][1000 genomes]
rs3129553	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3129557	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3129583	0.84[ASN][1000 genomes]
rs4654122	0.89[ASN][1000 genomes]
rs72762785	0.88[ASN][1000 genomes]
rs7520403	0.89[ASN][1000 genomes]
rs7539592	0.89[ASN][1000 genomes]
rs9426203	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9426250	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9426251	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv948348	chr1:246090818-246853200	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv1013800	chr1:246472691-246840960	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	nsv535409	chr1:246472691-246840960	Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
8	esv2762191	chr1:246546436-246815064	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv1002805	chr1:246608164-246890518	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv535413	chr1:246608164-246890518	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	nsv1010453	chr1:246645797-246815052	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv998579	chr1:246666041-246817877	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
13	nsv1010316	chr1:246686301-246840960	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv535414	chr1:246686301-246840960	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
15	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
16	nsv528615	chr1:246708467-246843315	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
17	nsv1014280	chr1:246709243-246823255	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
18	nsv1013264	chr1:246723012-246807400	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
19	nsv535415	chr1:246723012-246807400	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
20	nsv1005214	chr1:246730885-246841107	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
21	esv3368182	chr1:246770638-246799861	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
22	nsv1002595	chr1:246774036-246846548	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
23	nsv869936	chr1:246778181-246811161	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
24	nsv945431	chr1:246797617-246800231	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246739000-246806200	Weak transcription	Aorta	Aorta
2	chr1:246755400-246832800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr1:246774600-246800400	Weak transcription	Pancreas	Pancrea
4	chr1:246777000-246799800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:246777000-246802000	Weak transcription	NHEK	skin
6	chr1:246780800-246806400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr1:246780800-246813400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr1:246781000-246800000	Weak transcription	HMEC	breast
9	chr1:246781000-246803000	Weak transcription	Brain Anterior Caudate	brain
10	chr1:246781400-246800400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr1:246782000-246800400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:246782200-246810200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr1:246782400-246810800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:246782800-246810600	Weak transcription	Fetal Brain Male	brain
15	chr1:246784200-246810600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:246784200-246833800	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr1:246784400-246799800	Weak transcription	Spleen	Spleen
18	chr1:246785600-246800600	Weak transcription	Gastric	stomach
19	chr1:246785800-246801600	Weak transcription	Psoas Muscle	Psoas
20	chr1:246786000-246804800	Weak transcription	Fetal Heart	heart
21	chr1:246789200-246839200	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr1:246790800-246800400	Weak transcription	Right Ventricle	heart
23	chr1:246791000-246804800	Weak transcription	Small Intestine	intestine
24	chr1:246791000-246806200	Weak transcription	Brain Angular Gyrus	brain
25	chr1:246791200-246810400	Weak transcription	Brain Hippocampus Middle	brain
26	chr1:246791600-246800400	Weak transcription	Left Ventricle	heart
27	chr1:246792200-246801600	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr1:246792800-246802000	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr1:246793400-246800000	Weak transcription	Ovary	ovary
30	chr1:246795200-246803000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:246795200-246803200	Strong transcription	Primary T cells from cord blood	blood
32	chr1:246795200-246803400	Strong transcription	Primary B cells from peripheral blood	blood
33	chr1:246795200-246803400	Strong transcription	Liver	Liver
34	chr1:246795400-246802000	Strong transcription	Dnd41	blood
35	chr1:246795400-246803200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr1:246795600-246801800	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr1:246795600-246802800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr1:246795600-246802800	Strong transcription	Fetal Thymus	thymus
39	chr1:246795600-246803200	Strong transcription	Primary hematopoietic stem cells	blood
40	chr1:246795600-246803400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr1:246795600-246813600	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr1:246795800-246799800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr1:246795800-246800200	Weak transcription	Lung	lung
44	chr1:246796000-246799800	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr1:246796000-246831200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:246796200-246800000	Weak transcription	Fetal Muscle Trunk	muscle
47	chr1:246796200-246800000	Weak transcription	A549	lung
48	chr1:246796200-246806000	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr1:246796200-246822000	Weak transcription	Brain Substantia Nigra	brain
50	chr1:246796400-246800000	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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