Variant report

Variant	rs3870340
Chromosome Location	chr3:49536649-49536650
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49530765..49533090-chr3:49535053..49538549,4	K562	blood:
2	chr3:49536506..49538909-chr3:49540133..49543021,2	K562	blood:
3	chr3:49505597..49508548-chr3:49535239..49536958,2	MCF-7	breast:
4	chr3:49521377..49523560-chr3:49535457..49537721,2	K562	blood:

Variant related genes	Relation type
ENSG00000173402	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs11130197	1.00[YRI][hapmap]
rs11130201	0.94[AFR][1000 genomes]
rs11708174	0.82[ASW][hapmap];1.00[YRI][hapmap]
rs11717485	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1522929	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1568663	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17080495	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17080510	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17080567	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17080664	0.89[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1996874	0.82[ASW][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2131107	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2311794	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2311801	0.82[ASW][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2329024	0.82[ASW][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3870334	0.82[ASW][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3912831	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4241409	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs4452334	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855856	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855857	0.82[ASW][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855870	0.94[AFR][1000 genomes]
rs4855872	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855874	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855875	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855876	1.00[EUR][1000 genomes]
rs4855878	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855879	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs55808753	0.94[AFR][1000 genomes]
rs55990645	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56101322	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56760510	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56897974	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59579780	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60011446	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs61749312	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446269	0.92[AFR][1000 genomes]
rs6446270	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446271	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446273	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446276	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446278	0.87[YRI][hapmap];1.00[EUR][1000 genomes]
rs6446279	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446280	0.97[AFR][1000 genomes]
rs6446281	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446282	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446283	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6762593	0.82[ASW][hapmap];1.00[YRI][hapmap]
rs6766297	1.00[EUR][1000 genomes]
rs6787665	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6793124	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6797164	1.00[YRI][hapmap]
rs73830703	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73830704	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73830705	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73830706	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73831434	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73831435	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831436	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831437	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831438	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831439	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831440	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831441	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831442	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73834006	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7646393	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8179172	0.82[ASW][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9311441	0.94[AFR][1000 genomes]
rs9830627	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9837396	1.00[EUR][1000 genomes]
rs9861805	1.00[EUR][1000 genomes]
rs9869504	1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49509600-49537800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:49509800-49537600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr3:49509800-49547800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr3:49510000-49547800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:49514600-49548000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr3:49515400-49547800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:49515400-49547800	Weak transcription	Fetal Brain Female	brain
8	chr3:49515400-49548800	Weak transcription	Esophagus	oesophagus
9	chr3:49516800-49537600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:49517000-49547800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr3:49517200-49547800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr3:49522200-49547800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:49522400-49537800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:49522400-49548000	Weak transcription	Spleen	Spleen
15	chr3:49523400-49548000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr3:49523400-49548000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr3:49523600-49537000	Weak transcription	HMEC	breast
18	chr3:49523600-49537000	Weak transcription	HSMM	muscle
19	chr3:49523600-49537000	Weak transcription	NHDF-Ad	bronchial
20	chr3:49523600-49537600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:49523600-49548200	Weak transcription	Brain Substantia Nigra	brain
22	chr3:49526000-49547800	Weak transcription	Dnd41	blood
23	chr3:49526000-49548000	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr3:49526200-49537000	Weak transcription	NHEK	skin
25	chr3:49526200-49537800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:49527600-49547800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr3:49528200-49539600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:49529600-49568600	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr3:49530400-49547800	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr3:49531000-49548000	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr3:49531200-49538000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr3:49531200-49547800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr3:49531400-49537000	Weak transcription	Gastric	stomach
34	chr3:49531400-49537000	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr3:49531400-49539600	Weak transcription	Fetal Stomach	stomach
36	chr3:49531400-49547600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr3:49531400-49547800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr3:49531400-49547800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:49531400-49547800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr3:49531600-49537000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:49531600-49537000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr3:49531600-49537000	Weak transcription	Placenta	Placenta
43	chr3:49531600-49537000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:49531600-49537800	Weak transcription	Fetal Thymus	thymus
45	chr3:49531600-49539200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr3:49531600-49547800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr3:49531600-49547800	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr3:49531600-49547800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:49531800-49537800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:49531800-49537800	Weak transcription	Adipose Nuclei	Adipose

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