Variant report

Variant	rs3852673
Chromosome Location	chr2:96919642-96919643
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:96870008..96876069-chr2:96918284..96921014,6	K562	blood:
2	chr2:96916250..96917831-chr2:96918520..96920155,2	MCF-7	breast:
3	chr2:96918307..96920797-chr2:96930169..96933243,3	MCF-7	breast:
4	chr2:96916333..96921176-chr2:96924112..96927591,7	MCF-7	breast:
5	chr2:96870008..96877169-chr2:96918284..96921014,6	K562	blood:
6	chr2:96874452..96876033-chr2:96917329..96919794,2	MCF-7	breast:
7	chr2:96919042..96921310-chr2:96922215..96923771,2	K562	blood:
8	chr2:96917948..96919887-chr2:96921389..96924454,3	MCF-7	breast:
9	chr2:96918286..96920933-chr2:96930236..96932471,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000135956	Chromatin interaction
ENSG00000084090	Chromatin interaction
ENSG00000144021	Chromatin interaction
ENSG00000204685	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11551400	0.84[CEU][hapmap];0.92[GIH][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs12613263	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12617019	1.00[ASW][hapmap];0.94[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12618133	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2276650	0.94[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4371393	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4592891	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4826	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57476471	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59082429	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59664047	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60409279	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62152972	0.95[ASN][1000 genomes]
rs62153010	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62153011	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62153014	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62153018	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62153020	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62153022	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62153029	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6576968	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];1.00[ASN][1000 genomes]
rs6756208	0.93[ASN][1000 genomes]
rs72825854	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72825856	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72825864	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72825877	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73958180	0.95[ASN][1000 genomes]
rs7579709	0.94[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7580178	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs997547	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];0.95[ASN][1000 genomes]
rs997548	1.00[ASW][hapmap];0.94[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv834305	chr2:96848898-97019476	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	nsv874679	chr2:96860971-97184160	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3852673	TMEM127	cis	cerebellum	SCAN
rs3852673	ANKRD36B	cis	cerebellum	SCAN
rs3852673	CIAO1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96912200-96922400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr2:96914400-96920600	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr2:96914400-96924800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:96914400-96929800	Strong transcription	Fetal Stomach	stomach
5	chr2:96915200-96920400	Strong transcription	Primary T cells from cord blood	blood
6	chr2:96915200-96921000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr2:96915200-96921600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr2:96915200-96922000	Strong transcription	Thymus	Thymus
9	chr2:96915200-96922200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr2:96915400-96920600	Strong transcription	Primary B cells from cord blood	blood
11	chr2:96915400-96920600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr2:96915400-96925000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr2:96915600-96920200	Strong transcription	Primary B cells from peripheral blood	blood
14	chr2:96915600-96920200	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr2:96916000-96921800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr2:96916000-96924800	Strong transcription	Fetal Thymus	thymus
17	chr2:96916000-96929400	Strong transcription	Dnd41	blood
18	chr2:96916200-96919800	Strong transcription	Lung	lung
19	chr2:96916400-96921800	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:96916600-96922600	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr2:96916800-96920800	Genic enhancers	Monocytes-CD14+_RO01746	blood
22	chr2:96917000-96920400	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr2:96917000-96920400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr2:96917200-96921600	Strong transcription	NHEK	skin
25	chr2:96917200-96921800	Strong transcription	Fetal Brain Female	brain
26	chr2:96917200-96924200	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:96917400-96920800	Strong transcription	Placenta Amnion	Placenta Amnion
28	chr2:96917400-96921000	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr2:96917400-96921600	Strong transcription	GM12878-XiMat	blood
30	chr2:96917400-96929600	Strong transcription	Brain Germinal Matrix	brain
31	chr2:96917600-96919800	Strong transcription	Primary hematopoietic stem cells	blood
32	chr2:96917600-96920600	Genic enhancers	Duodenum Mucosa	Duodenum
33	chr2:96917600-96920800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
34	chr2:96917600-96920800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
35	chr2:96917600-96920800	Strong transcription	Brain Hippocampus Middle	brain
36	chr2:96917600-96921000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr2:96917600-96921000	Strong transcription	Ovary	ovary
38	chr2:96917600-96921200	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr2:96917600-96921200	Strong transcription	Colonic Mucosa	Colon
40	chr2:96917600-96921200	Strong transcription	K562	blood
41	chr2:96917600-96921800	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr2:96917600-96921800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr2:96917600-96922000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr2:96917600-96922600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr2:96917600-96923000	Strong transcription	Gastric	stomach
46	chr2:96917600-96923800	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr2:96917600-96924800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr2:96917600-96925600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr2:96917800-96919800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr2:96917800-96920000	Strong transcription	Brain Cingulate Gyrus	brain

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