Variant report

Variant	rs6712399
Chromosome Location	chr2:39636469-39636470
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39634850..39637298-chr2:39662502..39665371,4	K562	blood:
2	chr2:39635276..39640508-chr2:39640941..39645614,10	K562	blood:
3	chr2:39626974..39629375-chr2:39635445..39637433,2	MCF-7	breast:
4	chr2:39633573..39637306-chr2:39660675..39665702,6	MCF-7	breast:
5	chr2:39635276..39637954-chr2:39640941..39644825,4	K562	blood:
6	chr2:39635451..39641229-chr2:39641645..39645299,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231312	Chromatin interaction
ENSG00000011566	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10490305	0.89[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11886110	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11886434	0.85[AFR][1000 genomes]
rs11895366	0.93[AFR][1000 genomes]
rs11898704	1.00[ASW][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11902188	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17023620	0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs17038958	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2708227	1.00[JPT][hapmap]
rs3770661	0.83[ASN][1000 genomes]
rs55750780	0.82[AFR][1000 genomes]
rs55961227	0.98[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs56361338	0.83[ASN][1000 genomes]
rs56850142	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs56928728	0.95[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs57084694	0.84[AFR][1000 genomes]
rs58005382	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs58824151	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs59459399	0.95[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs59707152	0.83[ASN][1000 genomes]
rs59896787	0.84[AFR][1000 genomes]
rs60394429	0.93[AFR][1000 genomes]
rs61219633	0.92[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6544225	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6723987	0.90[AFR][1000 genomes]
rs6725784	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6727395	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6751506	1.00[ASW][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73923836	0.83[ASN][1000 genomes]
rs73923844	0.82[AFR][1000 genomes]
rs73923848	0.95[AMR][1000 genomes]
rs73923887	0.98[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs73923888	0.98[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs73923889	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73923895	0.97[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs73924011	0.85[AFR][1000 genomes]
rs73924013	0.85[AFR][1000 genomes]
rs73924016	0.84[AFR][1000 genomes]
rs73924810	0.83[ASN][1000 genomes]
rs73924815	0.83[ASN][1000 genomes]
rs73924816	0.83[ASN][1000 genomes]
rs73924817	0.83[ASN][1000 genomes]
rs73924818	0.83[ASN][1000 genomes]
rs7565210	0.90[AFR][1000 genomes]
rs7591563	0.98[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7595047	0.83[ASN][1000 genomes]
rs7599017	1.00[AFR][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	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic 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	21 gene(s)	inside rSNPs	diseases
2	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39603200-39638400	Weak transcription	Hela-S3	cervix
2	chr2:39607600-39643400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr2:39622600-39643600	Weak transcription	Brain Germinal Matrix	brain
4	chr2:39622800-39643200	Weak transcription	Fetal Brain Male	brain
5	chr2:39622800-39643400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr2:39627000-39636600	Weak transcription	Osteobl	bone
7	chr2:39627400-39636600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:39627400-39639600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr2:39630400-39637400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:39630800-39640600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:39631000-39638200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr2:39631600-39636800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr2:39631600-39637000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr2:39631600-39637200	Weak transcription	Fetal Muscle Leg	muscle
15	chr2:39631800-39638600	Weak transcription	Fetal Stomach	stomach
16	chr2:39632200-39637600	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr2:39632200-39638400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:39632400-39638600	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr2:39632400-39643400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr2:39632600-39639200	Enhancers	Adipose Nuclei	Adipose
21	chr2:39632600-39640400	Weak transcription	Brain Angular Gyrus	brain
22	chr2:39632600-39641400	Enhancers	Fetal Heart	heart
23	chr2:39632800-39637800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:39632800-39638400	Weak transcription	Brain Substantia Nigra	brain
25	chr2:39632800-39639600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:39633000-39636600	Weak transcription	HMEC	breast
27	chr2:39633000-39637200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:39633000-39638400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:39633000-39638400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:39633000-39640400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr2:39633000-39641200	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr2:39633000-39644400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr2:39633400-39636800	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr2:39633400-39636800	Weak transcription	NHEK	skin
35	chr2:39633400-39637800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr2:39633600-39636600	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr2:39633600-39637000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:39633600-39637200	Enhancers	NHDF-Ad	bronchial
39	chr2:39633600-39637800	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr2:39633600-39638000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr2:39633800-39637200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr2:39633800-39637400	Enhancers	NHLF	lung
43	chr2:39633800-39637600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr2:39634000-39636600	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr2:39634000-39636600	Weak transcription	Brain Anterior Caudate	brain
46	chr2:39634000-39637400	Enhancers	HepG2	liver
47	chr2:39634000-39637800	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr2:39634000-39639000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:39634200-39636800	Enhancers	Brain Hippocampus Middle	brain
50	chr2:39634400-39636600	Enhancers	Primary T cells from cord blood	blood

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