Variant report

Variant	rs3219112
Chromosome Location	chr1:226557504-226557505
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:226554977..226556502-chr1:226556594..226558224,2	MCF-7	breast:
2	chr1:226550494..226555291-chr1:226557365..226562090,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143799	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1104893	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1341333	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1341335	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1341336	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1397550	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1417765	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1805414	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1828445	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1828446	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1858548	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1858549	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1858550	0.80[AMR][1000 genomes]
rs1865220	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1865221	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1865222	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2027439	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2048424	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2048426	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2136875	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2249844	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2377313	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2570368	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2570369	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2570370	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2666427	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2666428	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2695235	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2695236	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2695237	0.82[AMR][1000 genomes]
rs2695238	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2695239	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2695240	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2793376	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2793377	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2793378	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2793380	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2793382	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2793654	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2793655	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2793657	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3219090	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3219110	0.88[AFR][1000 genomes]
rs3219119	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3754376	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs747657	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9426568	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226538400-226566800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:226543000-226558400	Strong transcription	Primary hematopoietic stem cells	blood
3	chr1:226543000-226578400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:226543000-226582800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:226543000-226590800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr1:226543000-226590800	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr1:226543000-226591400	Strong transcription	Primary T cells from cord blood	blood
8	chr1:226543200-226588600	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:226543200-226588600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:226543400-226580400	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr1:226543400-226590200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:226543400-226591400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:226543600-226590400	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr1:226543600-226591400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:226544200-226590400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr1:226544600-226580200	Strong transcription	Stomach Smooth Muscle	stomach
17	chr1:226544600-226580400	Strong transcription	Fetal Stomach	stomach
18	chr1:226544600-226591800	Strong transcription	Dnd41	blood
19	chr1:226544800-226558000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:226544800-226563400	Strong transcription	Spleen	Spleen
21	chr1:226544800-226590800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:226545000-226580400	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:226545000-226590800	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr1:226545200-226558600	Strong transcription	Brain Angular Gyrus	brain
25	chr1:226545200-226560000	Strong transcription	Colon Smooth Muscle	Colon
26	chr1:226545200-226569800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr1:226545200-226580200	Strong transcription	Ovary	ovary
28	chr1:226545200-226580400	Strong transcription	Fetal Intestine Large	intestine
29	chr1:226545200-226581000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr1:226545200-226581200	Strong transcription	Adipose Nuclei	Adipose
31	chr1:226545200-226582600	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr1:226545200-226582800	Strong transcription	Duodenum Mucosa	Duodenum
33	chr1:226545400-226560600	Strong transcription	Brain Anterior Caudate	brain
34	chr1:226545400-226560800	Strong transcription	Brain Inferior Temporal Lobe	brain
35	chr1:226545400-226568000	Strong transcription	Liver	Liver
36	chr1:226545400-226580000	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr1:226545400-226580200	Strong transcription	Thymus	Thymus
38	chr1:226545400-226580400	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr1:226545400-226580400	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr1:226545400-226580400	Strong transcription	Rectal Smooth Muscle	rectum
41	chr1:226545400-226581400	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr1:226545400-226584000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr1:226545400-226590600	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr1:226545600-226580200	Strong transcription	Esophagus	oesophagus
45	chr1:226545600-226581400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
46	chr1:226545600-226582800	Strong transcription	Fetal Thymus	thymus
47	chr1:226545600-226588200	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr1:226545800-226579800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:226545800-226579800	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr1:226545800-226580200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood

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