Variant report

Variant	rs3754376
Chromosome Location	chr1:226561064-226561065
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226560876..226565984-chr1:226590975..226596145,7	K562	blood:
2	chr1:226496099..226498370-chr1:226560413..226562179,2	MCF-7	breast:
3	chr1:226550494..226555291-chr1:226557365..226562090,4	MCF-7	breast:
4	chr1:226496175..226497867-chr1:226559586..226561925,2	MCF-7	breast:
5	chr1:226560810..226567347-chr1:226567516..226572343,10	K562	blood:

Variant related genes	Relation type
ENSG00000143799	Chromatin interaction
ENSG00000183814	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1104893	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11801168	0.83[CEU][hapmap];0.88[JPT][hapmap]
rs12567614	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs1341333	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1341335	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1341336	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1397550	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1417765	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1805414	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1828445	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1828446	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1858548	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1858549	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1858550	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1865220	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1865221	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1865222	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2027439	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2048424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2048426	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2136875	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2249844	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2377313	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2570368	0.83[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2570369	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2570370	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2666427	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2666428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2695235	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2695236	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2695237	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2695238	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2695239	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2695240	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2793376	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2793377	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2793378	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2793380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2793382	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2793654	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2793655	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2793657	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3219090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3219110	0.90[CHB][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes]
rs3219112	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3219119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6677172	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs747657	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs907186	0.88[JPT][hapmap]
rs9426568	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[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	nsv527874	chr1:226557878-226562779	Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers	TF binding region CpG island Chromatin interactive region	2 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	chr1:226543000-226578400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:226543000-226582800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:226543000-226590800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:226543000-226590800	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr1:226543000-226591400	Strong transcription	Primary T cells from cord blood	blood
7	chr1:226543200-226588600	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:226543200-226588600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:226543400-226580400	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr1:226543400-226590200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:226543400-226591400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:226543600-226590400	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr1:226543600-226591400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:226544200-226590400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr1:226544600-226580200	Strong transcription	Stomach Smooth Muscle	stomach
16	chr1:226544600-226580400	Strong transcription	Fetal Stomach	stomach
17	chr1:226544600-226591800	Strong transcription	Dnd41	blood
18	chr1:226544800-226563400	Strong transcription	Spleen	Spleen
19	chr1:226544800-226590800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:226545000-226580400	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr1:226545000-226590800	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr1:226545200-226569800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr1:226545200-226580200	Strong transcription	Ovary	ovary
24	chr1:226545200-226580400	Strong transcription	Fetal Intestine Large	intestine
25	chr1:226545200-226581000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr1:226545200-226581200	Strong transcription	Adipose Nuclei	Adipose
27	chr1:226545200-226582600	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr1:226545200-226582800	Strong transcription	Duodenum Mucosa	Duodenum
29	chr1:226545400-226568000	Strong transcription	Liver	Liver
30	chr1:226545400-226580000	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr1:226545400-226580200	Strong transcription	Thymus	Thymus
32	chr1:226545400-226580400	Strong transcription	H9 Cell Line	embryonic stem cell
33	chr1:226545400-226580400	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr1:226545400-226580400	Strong transcription	Rectal Smooth Muscle	rectum
35	chr1:226545400-226581400	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr1:226545400-226584000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr1:226545400-226590600	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr1:226545600-226580200	Strong transcription	Esophagus	oesophagus
39	chr1:226545600-226581400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
40	chr1:226545600-226582800	Strong transcription	Fetal Thymus	thymus
41	chr1:226545600-226588200	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr1:226545800-226579800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:226545800-226579800	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr1:226545800-226580200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr1:226545800-226580200	Strong transcription	Pancreas	Pancrea
46	chr1:226545800-226581800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr1:226545800-226582600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:226546000-226578200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:226546000-226578400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:226546000-226579800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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