Variant report

Variant	rs1561231
Chromosome Location	chr2:55455867-55455868
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55346562..55348270-chr2:55453778..55456492,2	K562	blood:
2	chr2:55450659..55454031-chr2:55454419..55456893,3	K562	blood:

Variant related genes	Relation type
ENSG00000227799	Chromatin interaction
ENSG00000162994	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10176839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10183953	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10191785	1.00[CEU][hapmap]
rs10439479	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11694920	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11892007	0.82[JPT][hapmap]
rs11904107	0.82[JPT][hapmap]
rs12104902	0.82[JPT][hapmap]
rs12105731	0.82[JPT][hapmap]
rs12464094	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs12470507	1.00[YRI][hapmap]
rs12617316	0.82[JPT][hapmap]
rs12713290	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13031346	0.82[JPT][hapmap]
rs1437387	0.82[JPT][hapmap]
rs1437388	0.82[JPT][hapmap]
rs1437389	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1437392	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1561232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17046834	0.82[JPT][hapmap]
rs17046915	1.00[CEU][hapmap]
rs2028138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2043714	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2118283	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2164715	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2249856	0.82[JPT][hapmap]
rs2289168	0.82[JPT][hapmap]
rs2576692	0.82[JPT][hapmap]
rs2576693	0.82[JPT][hapmap]
rs2576699	0.82[JPT][hapmap]
rs2576702	0.82[JPT][hapmap]
rs2576723	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2589060	0.82[JPT][hapmap]
rs2589061	0.82[JPT][hapmap]
rs2589063	0.82[JPT][hapmap]
rs2589081	1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2589082	1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2589083	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2589097	0.87[EUR][1000 genomes]
rs2589098	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2589111	0.82[JPT][hapmap]
rs2589113	0.82[JPT][hapmap]
rs2920845	0.86[EUR][1000 genomes]
rs2920846	0.83[EUR][1000 genomes]
rs2920869	0.86[EUR][1000 genomes]
rs2966465	0.82[JPT][hapmap]
rs2968816	0.82[JPT][hapmap]
rs2968820	0.82[JPT][hapmap]
rs2972087	0.82[JPT][hapmap]
rs4233959	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4591380	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6545476	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6545479	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6545482	0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs6545484	0.82[JPT][hapmap]
rs6713058	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6715694	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6716066	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6718747	0.82[JPT][hapmap]
rs6719579	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6723870	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6726732	0.82[JPT][hapmap]
rs6733567	0.82[JPT][hapmap]
rs6746287	0.82[JPT][hapmap]
rs6746757	1.00[CEU][hapmap]
rs6746983	1.00[CEU][hapmap]
rs6747682	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6747974	1.00[CEU][hapmap]
rs6750501	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6754605	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6759310	1.00[CEU][hapmap]
rs6759957	1.00[CEU][hapmap]
rs9784090	0.82[JPT][hapmap]

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	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3348896	chr2:55429540-55498552	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55451000-55457200	Weak transcription	NHDF-Ad	bronchial
2	chr2:55451000-55457600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:55451000-55457600	Weak transcription	HMEC	breast
4	chr2:55451000-55457800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:55451000-55457800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr2:55451000-55458000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:55451000-55458000	Weak transcription	Osteobl	bone
8	chr2:55451000-55458400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr2:55451000-55458400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr2:55451000-55458400	Weak transcription	Aorta	Aorta
11	chr2:55451000-55458400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:55451000-55458400	Weak transcription	Fetal Brain Female	brain
13	chr2:55451000-55458600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:55451000-55458600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr2:55451000-55458800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:55451000-55458800	Weak transcription	Esophagus	oesophagus
17	chr2:55451000-55458800	Weak transcription	Stomach Mucosa	stomach
18	chr2:55451200-55458400	Weak transcription	Fetal Kidney	kidney
19	chr2:55451200-55458400	Weak transcription	Fetal Lung	lung
20	chr2:55451400-55458400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr2:55451400-55458400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr2:55451400-55458600	Weak transcription	Colon Smooth Muscle	Colon
23	chr2:55451400-55458800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr2:55451600-55456600	Weak transcription	A549	lung
25	chr2:55451600-55457800	Weak transcription	Placenta	Placenta
26	chr2:55451800-55458400	Weak transcription	Brain Angular Gyrus	brain
27	chr2:55451800-55458600	Weak transcription	Fetal Intestine Small	intestine
28	chr2:55452200-55458600	Weak transcription	Fetal Muscle Leg	muscle
29	chr2:55452400-55456600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:55452400-55458400	Weak transcription	Fetal Stomach	stomach
31	chr2:55452600-55457600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr2:55452600-55458400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr2:55452600-55458400	Weak transcription	Brain Germinal Matrix	brain
34	chr2:55452800-55458400	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr2:55453000-55456000	Weak transcription	Left Ventricle	heart
36	chr2:55453000-55457800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr2:55453000-55458400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr2:55453000-55458400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr2:55453000-55458600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:55453000-55458600	Weak transcription	Lung	lung
41	chr2:55453000-55458600	Weak transcription	Pancreas	Pancrea
42	chr2:55453000-55458800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr2:55453200-55458400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr2:55453800-55456200	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr2:55454400-55456000	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr2:55454400-55456000	Enhancers	Primary B cells from peripheral blood	blood
47	chr2:55454400-55456200	Enhancers	Primary T cells fromperipheralblood	blood
48	chr2:55454800-55456000	Enhancers	Primary hematopoietic stem cells	blood
49	chr2:55454800-55456000	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr2:55454800-55456000	Enhancers	HUVEC	blood vessel

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