Variant report

Variant	rs12999966
Chromosome Location	chr2:55877214-55877215
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PAX5	chr2:55877170-55877672	GM12878	blood:	n/a	n/a
2	PAX5	chr2:55877210-55877533	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55876589..55879257-chr2:55911121..55913801,2	K562	blood:

Variant related genes	Relation type
PNPT1	TF binding region

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1013138	0.84[CHB][hapmap];0.82[ASN][1000 genomes]
rs12329050	0.81[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs12473585	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12473621	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12612227	0.86[ASN][1000 genomes]
rs12617627	0.96[YRI][hapmap]
rs12618859	0.85[CHB][hapmap];0.96[YRI][hapmap];0.85[ASN][1000 genomes]
rs12619903	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12620407	0.89[ASN][1000 genomes]
rs12623937	0.85[CHB][hapmap]
rs12986444	0.86[ASN][1000 genomes]
rs12986797	0.86[ASN][1000 genomes]
rs12992408	0.92[YRI][hapmap]
rs12993624	0.83[JPT][hapmap];0.88[YRI][hapmap];0.83[ASN][1000 genomes]
rs12993839	0.81[CHB][hapmap]
rs12994656	0.81[CHB][hapmap]
rs12998664	0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs12998780	0.86[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs12999506	0.81[ASN][1000 genomes]
rs13001425	0.90[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13002860	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13004436	0.81[CHB][hapmap]
rs13005850	0.84[ASN][1000 genomes]
rs13007577	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13009447	0.89[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13009906	0.81[CEU][hapmap];0.92[YRI][hapmap]
rs13010217	0.85[CHB][hapmap];0.83[JPT][hapmap];0.96[YRI][hapmap];0.88[ASN][1000 genomes]
rs13013133	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13013699	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13014898	0.88[YRI][hapmap]
rs13015744	0.90[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs13018767	0.81[ASN][1000 genomes]
rs13019595	0.86[ASN][1000 genomes]
rs13021958	0.90[YRI][hapmap]
rs13024761	0.81[ASN][1000 genomes]
rs13025331	0.85[CHB][hapmap];0.83[JPT][hapmap];0.96[YRI][hapmap];0.85[ASN][1000 genomes]
rs13027095	0.85[ASN][1000 genomes]
rs13027803	0.84[ASN][1000 genomes]
rs13027853	0.84[ASN][1000 genomes]
rs13030396	0.81[CHB][hapmap]
rs13032503	0.81[CEU][hapmap];0.92[YRI][hapmap]
rs1318672	0.81[YRI][hapmap]
rs1443746	0.95[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs1542643	0.81[ASN][1000 genomes]
rs17737233	0.85[CHB][hapmap];0.86[ASN][1000 genomes]
rs17800203	0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs1822513	0.86[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2291336	0.85[CHB][hapmap];0.86[ASN][1000 genomes]
rs34129478	0.86[ASN][1000 genomes]
rs34513671	0.86[AFR][1000 genomes]
rs34679603	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35124901	0.86[ASN][1000 genomes]
rs35255044	0.86[ASN][1000 genomes]
rs35968359	0.83[ASN][1000 genomes]
rs3791654	0.85[CHB][hapmap];0.83[JPT][hapmap];0.92[YRI][hapmap];0.86[ASN][1000 genomes]
rs3828238	0.85[CHB][hapmap];0.86[ASN][1000 genomes]
rs4322879	0.81[CHB][hapmap];0.83[JPT][hapmap];0.96[YRI][hapmap];0.86[ASN][1000 genomes]
rs5012561	0.82[CEU][hapmap];0.92[YRI][hapmap]
rs56122729	0.88[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6737995	0.96[YRI][hapmap];0.86[ASN][1000 genomes]
rs6753530	0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs6757006	0.88[CEU][hapmap];0.88[YRI][hapmap]
rs7575170	1.00[CEU][hapmap];0.82[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7592219	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7596377	0.89[CEU][hapmap]
rs8080	0.87[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1008452	chr2:55809191-55987274	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv9791	chr2:55872725-55883751	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55846800-55919800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:55847400-55911000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:55847600-55886600	Weak transcription	Stomach Mucosa	stomach
4	chr2:55849800-55882800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:55853600-55882400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr2:55858200-55920400	Weak transcription	Fetal Heart	heart
7	chr2:55859400-55877600	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr2:55860400-55905400	Weak transcription	Fetal Brain Male	brain
9	chr2:55862000-55877800	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr2:55864000-55893200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:55864200-55882800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr2:55864400-55919600	Weak transcription	NHLF	lung
13	chr2:55864600-55881400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr2:55864600-55881400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr2:55864800-55879200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr2:55865000-55880400	Weak transcription	HMEC	breast
17	chr2:55866200-55882400	Weak transcription	Ovary	ovary
18	chr2:55866600-55920000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr2:55868000-55879200	Weak transcription	NH-A	brain
20	chr2:55870400-55887600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:55870400-55887800	Weak transcription	Fetal Brain Female	brain
22	chr2:55870400-55920000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr2:55870600-55879800	Weak transcription	HUVEC	blood vessel
24	chr2:55870600-55881400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr2:55870600-55892800	Weak transcription	Psoas Muscle	Psoas
26	chr2:55870600-55920000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr2:55870800-55879200	Weak transcription	Brain Hippocampus Middle	brain
28	chr2:55870800-55888000	Weak transcription	Colonic Mucosa	Colon
29	chr2:55870800-55893400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:55870800-55903600	Weak transcription	Gastric	stomach
31	chr2:55870800-55909000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:55870800-55920400	Weak transcription	Aorta	Aorta
33	chr2:55871000-55879000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr2:55871000-55880000	Weak transcription	Right Ventricle	heart
35	chr2:55871000-55880600	Weak transcription	Lung	lung
36	chr2:55871000-55887800	Weak transcription	Esophagus	oesophagus
37	chr2:55871000-55893200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr2:55871000-55893200	Weak transcription	Thymus	Thymus
39	chr2:55871000-55920000	Weak transcription	Spleen	Spleen
40	chr2:55871200-55879000	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr2:55871200-55879200	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr2:55871200-55880000	Weak transcription	Brain Substantia Nigra	brain
43	chr2:55871200-55880400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr2:55871200-55880600	Weak transcription	Colon Smooth Muscle	Colon
45	chr2:55871200-55893400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr2:55871200-55905200	Weak transcription	Brain Angular Gyrus	brain
47	chr2:55871400-55882600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr2:55871400-55905200	Weak transcription	Fetal Kidney	kidney
49	chr2:55872000-55879200	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr2:55873000-55879000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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