Variant report

Variant	rs3754744
Chromosome Location	chr2:174002064-174002065
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:173996961..173999501-chr2:174001497..174003387,2	K562	blood:
2	chr2:173938869..173942300-chr2:173999393..174002549,3	K562	blood:
3	chr2:174001713..174004612-chr2:174011601..174013779,2	K562	blood:
4	chr2:173984313..173986145-chr2:174000208..174002832,2	K562	blood:

Variant related genes	Relation type
ENSG00000091436	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10187560	0.82[CHD][hapmap]
rs10930579	0.94[ASN][1000 genomes]
rs12615166	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12986917	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12987496	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12989116	1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12990553	0.89[ASN][1000 genomes]
rs12997078	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12998711	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13004212	0.86[ASN][1000 genomes]
rs13008554	0.84[ASN][1000 genomes]
rs13017210	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs13017438	0.94[ASN][1000 genomes]
rs13020796	0.81[EUR][1000 genomes]
rs13022800	0.90[CHB][hapmap];1.00[YRI][hapmap]
rs13029949	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13032010	1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs16861278	0.89[CHB][hapmap]
rs17302977	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17761169	0.82[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs2076857	0.99[ASN][1000 genomes]
rs2278883	0.82[CHB][hapmap];0.81[CHD][hapmap];0.81[ASN][1000 genomes]
rs2289397	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2289399	1.00[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.94[ASN][1000 genomes]
rs34014656	0.81[ASN][1000 genomes]
rs34472765	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34658268	0.87[ASN][1000 genomes]
rs34681024	0.83[ASN][1000 genomes]
rs34702663	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34862313	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35250703	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36102078	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs36103648	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3754741	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.94[ASN][1000 genomes]
rs3754743	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3769157	0.88[ASN][1000 genomes]
rs3769161	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3769167	1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs3769187	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3769192	0.82[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3769194	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3769199	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3769203	0.87[CEU][hapmap];0.90[CHB][hapmap];0.90[TSI][hapmap]
rs4972533	0.82[ASW][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs55913048	0.94[ASN][1000 genomes]
rs56151459	0.98[ASN][1000 genomes]
rs56193548	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56342397	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6433395	0.90[CHB][hapmap]
rs67422536	0.83[AFR][1000 genomes]
rs67683956	0.82[ASN][1000 genomes]
rs71417423	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72905080	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011724	chr2:173916482-174231908	Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv834460	chr2:173919464-174085288	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv834461	chr2:173979734-174038471	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173974400-174005200	Weak transcription	Fetal Intestine Small	intestine
2	chr2:173982800-174006400	Weak transcription	Fetal Lung	lung
3	chr2:173988200-174004600	Weak transcription	Fetal Intestine Large	intestine
4	chr2:173989200-174006000	Weak transcription	Primary B cells from cord blood	blood
5	chr2:173989600-174003800	Weak transcription	Right Ventricle	heart
6	chr2:173989600-174007600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:173991800-174005200	Weak transcription	K562	blood
8	chr2:173996600-174012800	Weak transcription	Ovary	ovary
9	chr2:173996600-174013400	Weak transcription	Aorta	Aorta
10	chr2:173997400-174003400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr2:173998800-174002800	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr2:173999200-174002200	Enhancers	Dnd41	blood
13	chr2:173999400-174002200	Enhancers	HMEC	breast
14	chr2:173999400-174003000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:174000800-174002200	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr2:174000800-174002200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr2:174000800-174002200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr2:174000800-174002200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:174000800-174002400	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr2:174000800-174002600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr2:174000800-174002800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr2:174001000-174002200	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr2:174001000-174002600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:174001200-174002200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr2:174001200-174002200	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr2:174001200-174002200	Enhancers	Fetal Brain Male	brain
27	chr2:174001200-174003000	Enhancers	GM12878-XiMat	blood
28	chr2:174001200-174005400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr2:174001400-174002200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr2:174001400-174002200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr2:174001400-174002200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:174001400-174002200	Enhancers	Fetal Brain Female	brain
33	chr2:174001400-174002600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:174001400-174002600	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr2:174001400-174002600	Enhancers	NHDF-Ad	bronchial
36	chr2:174001400-174005200	Weak transcription	A549	lung
37	chr2:174001600-174002200	Enhancers	NHEK	skin
38	chr2:174001600-174002400	Enhancers	Primary T cells from cord blood	blood
39	chr2:174001600-174003200	Weak transcription	Fetal Heart	heart
40	chr2:174001600-174006000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr2:174001600-174012800	Weak transcription	Left Ventricle	heart
42	chr2:174001600-174013200	Weak transcription	HUVEC	blood vessel
43	chr2:174001800-174002200	Enhancers	Osteobl	bone
44	chr2:174001800-174002800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr2:174001800-174002800	Weak transcription	Psoas Muscle	Psoas
46	chr2:174001800-174003000	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr2:174001800-174003400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr2:174001800-174003400	Weak transcription	Stomach Smooth Muscle	stomach
49	chr2:174001800-174003800	Weak transcription	Colon Smooth Muscle	Colon
50	chr2:174001800-174005400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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