Variant report

Variant	rs3811040
Chromosome Location	chr2:113498566-113498567
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113490480..113492391-chr2:113497209..113499304,2	MCF-7	breast:
2	chr2:113498551..113500379-chr2:113500428..113502651,2	MCF-7	breast:
3	chr2:113494174..113497149-chr2:113498169..113501169,3	K562	blood:
4	chr2:113497949..113500528-chr2:113517759..113519834,2	MCF-7	breast:
5	chr2:113492043..113493999-chr2:113497953..113500095,2	K562	blood:
6	chr2:113498169..113499774-chr2:113578682..113581202,2	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10165537	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10187872	0.86[CHB][hapmap];0.84[GIH][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs10193063	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10200192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10203064	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10496444	0.81[CHB][hapmap]
rs10496445	0.81[CHB][hapmap]
rs11123148	0.86[CHB][hapmap];0.83[EUR][1000 genomes]
rs11123149	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12463996	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12475027	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12478842	0.81[CHB][hapmap]
rs12622683	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12711741	0.81[CHB][hapmap]
rs13008855	1.00[YRI][hapmap]
rs13009294	0.81[CHB][hapmap]
rs13013602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13015273	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13016817	0.96[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13019249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13026263	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][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];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13027814	0.81[CHB][hapmap]
rs13036237	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13382217	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13429613	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1609682	0.81[CHB][hapmap]
rs17649681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2071373	0.81[CHB][hapmap];1.00[YRI][hapmap]
rs2138606	0.81[CHB][hapmap]
rs2862226	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3783521	0.81[CHB][hapmap];1.00[YRI][hapmap]
rs3783525	0.81[CHB][hapmap]
rs3783526	0.81[CHB][hapmap];1.00[YRI][hapmap]
rs3783546	0.81[CHB][hapmap]
rs3783550	0.81[CHB][hapmap]
rs3827761	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4261731	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4848298	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][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];0.98[ASN][1000 genomes]
rs4848301	0.80[CHB][hapmap]
rs4848302	0.81[CHB][hapmap]
rs4849115	0.81[CHB][hapmap];1.00[YRI][hapmap]
rs4849118	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55762606	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58694576	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6542095	0.81[CHB][hapmap]
rs6706663	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6712572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6721044	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6721292	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6753803	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7577241	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7591704	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7594852	0.94[EUR][1000 genomes]
rs7599690	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7607470	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs908551	1.00[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]

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	nsv428724	chr2:113376894-113555421	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv1010106	chr2:113394981-113556071	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3811040	ZC3H6	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113484400-113507400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:113484600-113507600	Weak transcription	Colonic Mucosa	Colon
3	chr2:113484800-113507600	Weak transcription	Primary B cells from cord blood	blood
4	chr2:113486600-113511600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr2:113488200-113507400	Weak transcription	Spleen	Spleen
6	chr2:113491000-113520800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:113491400-113498800	Weak transcription	Fetal Kidney	kidney
8	chr2:113491800-113507200	Weak transcription	Fetal Brain Female	brain
9	chr2:113492200-113512000	Weak transcription	Fetal Heart	heart
10	chr2:113492400-113507600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr2:113494200-113506400	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr2:113494200-113507400	Strong transcription	Fetal Thymus	thymus
13	chr2:113494200-113519600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:113494400-113500000	Strong transcription	Fetal Muscle Trunk	muscle
15	chr2:113494400-113505800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:113494400-113521000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr2:113494600-113502400	Strong transcription	Fetal Stomach	stomach
18	chr2:113494600-113506400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:113494800-113505400	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr2:113494800-113506000	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr2:113494800-113506200	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr2:113494800-113507000	Strong transcription	Dnd41	blood
23	chr2:113494800-113520000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:113495000-113500000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:113495200-113500400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr2:113495200-113500600	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr2:113495200-113504200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr2:113495400-113499200	Strong transcription	Fetal Muscle Leg	muscle
29	chr2:113495600-113499800	Weak transcription	Hela-S3	cervix
30	chr2:113495600-113500400	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr2:113495600-113500400	Strong transcription	HSMM	muscle
32	chr2:113495600-113502400	Strong transcription	Thymus	Thymus
33	chr2:113495800-113499000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr2:113495800-113500400	Strong transcription	GM12878-XiMat	blood
35	chr2:113495800-113500400	Strong transcription	NH-A	brain
36	chr2:113495800-113502800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr2:113495800-113503600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:113495800-113504200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr2:113495800-113505400	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr2:113495800-113505400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr2:113495800-113505600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr2:113495800-113521400	Weak transcription	Small Intestine	intestine
43	chr2:113496000-113500400	Strong transcription	Primary hematopoietic stem cells	blood
44	chr2:113496000-113500400	Strong transcription	HepG2	liver
45	chr2:113496000-113521200	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr2:113496000-113521200	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr2:113496200-113499400	Strong transcription	Placenta	Placenta
48	chr2:113496200-113499800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr2:113496200-113502800	Strong transcription	NHDF-Ad	bronchial
50	chr2:113496200-113507400	Weak transcription	Primary T cells from cord blood	blood

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