Variant report

Variant	rs1341336
Chromosome Location	chr1:226596389-226596390
allele	A/G
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	chr1:226594217-226596471	A549	lung:	n/a	chr1:226595895-226595908 chr1:226595717-226595730 chr1:226594733-226594746
2	POLR2A	chr1:226594891-226596463	SK-N-MC	brain:	n/a	n/a
3	ELF1	chr1:226595190-226596430	GM12878	blood:	n/a	chr1:226595931-226595943 chr1:226595763-226595775 chr1:226595685-226595694 chr1:226596392-226596404
4	POLR2A	chr1:226594992-226596435	GM12892	blood:	n/a	n/a
5	MAX	chr1:226594985-226596390	A549	lung:	n/a	n/a
6	POLR2A	chr1:226595556-226596660	HCT-116	colon:	n/a	n/a
7	POLR2A	chr1:226595114-226596592	GM12892	blood:	n/a	n/a
8	JUN	chr1:226593026-226596854	K562	blood:	n/a	n/a
9	POLR2A	chr1:226595083-226596533	GM18505	blood:	n/a	n/a
10	HCFC1	chr1:226595050-226596409	K562	blood:	n/a	n/a
11	MAX	chr1:226594962-226596461	K562	blood:	n/a	chr1:226596391-226596401
12	YY1	chr1:226595205-226596538	SK-N-SH	brain:	n/a	chr1:226595364-226595378
13	KAP1	chr1:226594226-226596440	HEK293	kidney:	n/a	n/a
14	KAP1	chr1:226594958-226596457	U2OS	brain:	n/a	n/a
15	POLR2A	chr1:226595118-226596393	HEK293	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:226495420..226500064-chr1:226594005..226597004,6	K562	blood:
2	chr1:226496316..226500064-chr1:226594874..226597502,3	K562	blood:
3	chr1:226595064..226597397-chr1:226599345..226601411,3	MCF-7	breast:
4	chr1:226594983..226596955-chr1:227126462..227129196,3	K562	blood:
5	chr1:226594724..226598216-chr1:226599325..226601512,4	K562	blood:
6	chr1:226595397..226597205-chr1:226598712..226600221,2	MCF-7	breast:
7	chr1:226593987..226597015-chr1:226736474..226738189,3	MCF-7	breast:

Variant related genes	Relation type
PARP1	TF binding region
ENSG00000163050	Chromatin interaction
ENSG00000270287	Chromatin interaction
ENSG00000203685	Chromatin interaction
ENSG00000183814	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1104893	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1341333	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1341335	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1397550	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1417765	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1805414	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1828445	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1828446	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1858548	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1858549	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1858550	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1865220	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1865221	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1865222	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2027439	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2048424	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2048426	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2136875	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2249844	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2570368	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2570369	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2570370	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2666427	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2666428	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2695235	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2695236	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2695237	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2695238	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2695239	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2695240	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2793376	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2793377	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2793378	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2793380	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2793382	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2793654	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2793655	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2793657	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3219090	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3219112	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3219119	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3754376	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs907186	0.81[ASN][1000 genomes]
rs9426568	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832770	chr1:226465130-226655512	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv832781	chr1:226570901-226750697	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS 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	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226592600-226596400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:226592800-226596400	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr1:226593000-226596400	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr1:226594000-226596400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:226594200-226596400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr1:226594200-226596400	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr1:226594200-226596600	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr1:226594400-226596400	Active TSS	H9 Cell Line	embryonic stem cell
9	chr1:226594400-226596400	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr1:226594400-226596400	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr1:226594600-226596400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:226594800-226596400	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr1:226594800-226596400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:226594800-226596400	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr1:226594800-226596400	Active TSS	Colon Smooth Muscle	Colon
16	chr1:226594800-226596400	Active TSS	Duodenum Mucosa	Duodenum
17	chr1:226594800-226596400	Active TSS	Ovary	ovary
18	chr1:226594800-226596400	Active TSS	HSMM	muscle
19	chr1:226594800-226596600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:226595000-226596400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:226595000-226596400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:226595000-226596400	Active TSS	Liver	Liver
23	chr1:226595000-226596400	Active TSS	Brain Anterior Caudate	brain
24	chr1:226595000-226596400	Active TSS	Brain Cingulate Gyrus	brain
25	chr1:226595000-226596400	Active TSS	Colonic Mucosa	Colon
26	chr1:226595000-226596400	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr1:226595000-226596400	Active TSS	Fetal Stomach	stomach
28	chr1:226595000-226596400	Active TSS	Psoas Muscle	Psoas
29	chr1:226595000-226596400	Active TSS	Rectal Mucosa Donor 31	rectum
30	chr1:226595000-226596400	Active TSS	Rectal Smooth Muscle	rectum
31	chr1:226595000-226596400	Active TSS	Stomach Smooth Muscle	stomach
32	chr1:226595000-226596600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:226595000-226596600	Active TSS	Hela-S3	cervix
34	chr1:226595200-226596400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:226595200-226596400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr1:226595200-226596400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:226595200-226596400	Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr1:226595200-226596400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr1:226595200-226596400	Active TSS	Brain Hippocampus Middle	brain
40	chr1:226595200-226596400	Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr1:226595200-226596400	Active TSS	Monocytes-CD14+_RO01746	blood
42	chr1:226595200-226596400	Active TSS	Osteobl	bone
43	chr1:226595200-226596600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:226595200-226596600	Active TSS	Rectal Mucosa Donor 29	rectum
45	chr1:226595400-226596400	Active TSS	Primary neutrophils fromperipheralblood	blood
46	chr1:226595400-226607000	Weak transcription	Fetal Brain Male	brain
47	chr1:226595800-226596400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
48	chr1:226596000-226596400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
49	chr1:226596000-226596400	Flanking Active TSS	Primary B cells from peripheral blood	blood
50	chr1:226596000-226596400	Flanking Active TSS	Primary T cells fromperipheralblood	blood

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