Variant report

Variant	rs3754835
Chromosome Location	chr2:32206029-32206030
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:32202781..32206139-chr2:32208630..32212178,4	MCF-7	breast:
2	chr2:32205175..32207805-chr2:32210212..32212812,3	K562	blood:
3	chr2:32201417..32203773-chr2:32204929..32208993,3	K562	blood:
4	chr2:32185724..32188671-chr2:32204592..32206749,2	MCF-7	breast:
5	chr2:32201417..32203517-chr2:32206018..32209549,4	K562	blood:
6	chr2:32204041..32206611-chr2:32221999..32224174,3	K562	blood:

Variant related genes	Relation type
ENSG00000162959	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11124272	0.95[CHB][hapmap];0.98[CHD][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs11691939	0.95[CHB][hapmap];0.95[CHD][hapmap]
rs12478134	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs12991444	0.95[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap]
rs13006495	1.00[CHB][hapmap];0.95[CHD][hapmap]
rs13013695	1.00[CHB][hapmap];0.95[CHD][hapmap]
rs17011801	0.95[CHB][hapmap]
rs2280968	1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap]
rs2366547	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs34197800	1.00[CHB][hapmap];0.95[CHD][hapmap]
rs3769605	0.95[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap]
rs3769611	0.82[CHD][hapmap]
rs4952244	0.86[CHB][hapmap]
rs61399065	0.91[ASN][1000 genomes]

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	nsv532648	chr2:31591498-32312698	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv949102	chr2:32030307-33011548	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3754835	FAM179A	cis	cerebellum	SCAN
rs3754835	SLC30A6	cis	cerebellum	SCAN
rs3754835	SLC30A6	cis	parietal	SCAN
rs3754835	NLRC4	cis	lymphoblastoid	seeQTL

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32168400-32212200	Weak transcription	Esophagus	oesophagus
2	chr2:32168400-32233400	Weak transcription	Fetal Stomach	stomach
3	chr2:32171000-32227600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:32185200-32209600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:32186600-32212200	Weak transcription	HMEC	breast
6	chr2:32186800-32208000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:32187000-32211400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:32187200-32212000	Weak transcription	Ovary	ovary
9	chr2:32187400-32210600	Weak transcription	Aorta	Aorta
10	chr2:32191600-32234200	Weak transcription	Lung	lung
11	chr2:32193600-32206400	Weak transcription	Hela-S3	cervix
12	chr2:32193600-32212200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:32193600-32212800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:32193800-32209400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:32195200-32210400	Weak transcription	Fetal Intestine Small	intestine
16	chr2:32202400-32233600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr2:32203800-32223000	Weak transcription	Spleen	Spleen
18	chr2:32204200-32206600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:32204200-32206600	Enhancers	Primary B cells from peripheral blood	blood
20	chr2:32204800-32206600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:32204800-32206600	Enhancers	Muscle Satellite Cultured Cells	--
22	chr2:32205000-32206200	Enhancers	Osteobl	bone
23	chr2:32205200-32206400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr2:32205200-32206400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr2:32205200-32206400	Enhancers	Fetal Muscle Leg	muscle
26	chr2:32205200-32206400	Enhancers	Psoas Muscle	Psoas
27	chr2:32205200-32206400	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr2:32205200-32206400	Enhancers	Small Intestine	intestine
29	chr2:32205200-32206800	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr2:32205200-32207200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr2:32205200-32207800	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr2:32205400-32206400	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr2:32205400-32206400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:32205400-32206600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:32205400-32207800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:32205400-32212800	Weak transcription	NH-A	brain
37	chr2:32205600-32206400	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr2:32205600-32206400	Enhancers	Primary hematopoietic stem cells	blood
39	chr2:32205600-32206400	Enhancers	Brain Substantia Nigra	brain
40	chr2:32205600-32206600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr2:32205600-32206600	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr2:32205600-32206600	Enhancers	NHEK	skin
43	chr2:32205600-32206800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr2:32205600-32206800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr2:32205600-32206800	Enhancers	Liver	Liver
46	chr2:32205600-32207000	Enhancers	A549	lung
47	chr2:32205600-32207000	Enhancers	K562	blood
48	chr2:32205600-32217600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr2:32205800-32206200	Enhancers	H9 Cell Line	embryonic stem cell
50	chr2:32205800-32206200	Flanking Active TSS	Primary B cells from cord blood	blood

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