Variant report

Variant	rs2289399
Chromosome Location	chr2:174055731-174055732
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10187560	0.81[CHD][hapmap]
rs10930579	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12615166	0.83[ASN][1000 genomes]
rs12986917	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[ASN][1000 genomes]
rs12987496	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs12989116	1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs12990553	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12997078	0.85[ASN][1000 genomes]
rs12998711	0.83[ASN][1000 genomes]
rs13004212	0.80[ASN][1000 genomes]
rs13008554	0.86[ASN][1000 genomes]
rs13017210	0.82[ASN][1000 genomes]
rs13017438	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13022800	0.90[CHB][hapmap]
rs13029949	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs13032010	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16861278	0.89[CHB][hapmap]
rs17302977	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[ASN][1000 genomes]
rs17761169	0.88[CEU][hapmap];0.82[CHB][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2076857	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2278883	0.82[CHB][hapmap]
rs2289397	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34472765	0.80[ASN][1000 genomes]
rs34658268	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34702663	0.81[ASN][1000 genomes]
rs35250703	0.80[ASN][1000 genomes]
rs36102078	0.80[ASN][1000 genomes]
rs36103648	0.85[ASN][1000 genomes]
rs3754741	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3754743	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3754744	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]
rs3769157	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3769161	0.81[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3769167	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3769187	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3769192	0.82[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.83[ASN][1000 genomes]
rs3769194	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs3769203	0.90[CHB][hapmap]
rs4972533	0.82[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55913048	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56151459	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56193548	0.80[ASN][1000 genomes]
rs6433395	0.90[CHB][hapmap]
rs71417423	0.83[ASN][1000 genomes]
rs72905080	0.80[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	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

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:174026000-174069000	Weak transcription	Primary B cells from cord blood	blood
2	chr2:174026600-174083200	Weak transcription	Esophagus	oesophagus
3	chr2:174046200-174055800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr2:174046400-174075800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr2:174046600-174055800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:174047000-174062800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:174047600-174056400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr2:174047600-174060800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:174047600-174062800	Weak transcription	GM12878-XiMat	blood
10	chr2:174047800-174065800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:174048600-174095200	Weak transcription	Thymus	Thymus
12	chr2:174049000-174070600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr2:174049200-174070200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr2:174049200-174083200	Weak transcription	Small Intestine	intestine
15	chr2:174049400-174055800	Weak transcription	Fetal Muscle Leg	muscle
16	chr2:174049400-174056000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:174049400-174058400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:174049400-174060600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr2:174049400-174060800	Weak transcription	Lung	lung
20	chr2:174049400-174060800	Weak transcription	Right Ventricle	heart
21	chr2:174049400-174078200	Weak transcription	HUVEC	blood vessel
22	chr2:174049600-174056000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr2:174049600-174056200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:174049600-174062800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:174049600-174074400	Weak transcription	Fetal Stomach	stomach
26	chr2:174049600-174079800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:174049800-174062600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:174050200-174062800	Weak transcription	HepG2	liver
29	chr2:174051600-174065200	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr2:174052000-174056200	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr2:174052000-174059600	Weak transcription	Aorta	Aorta
32	chr2:174052000-174063000	Weak transcription	Placenta	Placenta
33	chr2:174052200-174056000	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr2:174052200-174056000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr2:174052400-174055800	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr2:174052400-174056200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr2:174052800-174058600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr2:174052800-174063200	Weak transcription	Primary B cells from peripheral blood	blood
39	chr2:174053000-174056400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:174053000-174057400	Strong transcription	Hela-S3	cervix
41	chr2:174053000-174065400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr2:174053200-174055800	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr2:174053200-174055800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr2:174053200-174058400	Weak transcription	HSMM	muscle
45	chr2:174053400-174055800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:174053400-174055800	Weak transcription	Fetal Lung	lung
47	chr2:174053400-174055800	Weak transcription	Rectal Smooth Muscle	rectum
48	chr2:174053400-174055800	Weak transcription	HMEC	breast
49	chr2:174053400-174056000	Weak transcription	NH-A	brain
50	chr2:174053400-174056400	Weak transcription	Stomach Smooth Muscle	stomach

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