Variant report

Variant	rs6431262
Chromosome Location	chr2:234199537-234199538
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:234198551..234200102-chr2:234262598..234264638,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243637	Chromatin interaction
ENSG00000077044	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1045095	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10929033	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11685932	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs11894529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13005285	0.80[CEU][hapmap];0.86[CHB][hapmap]
rs1816753	0.84[ASN][1000 genomes]
rs2119504	0.84[ASN][1000 genomes]
rs2241876	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2241877	0.94[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.84[MEX][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2289475	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35812841	0.86[ASN][1000 genomes]
rs3749079	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3792110	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4663136	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4663429	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6431259	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6431655	0.89[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap]
rs6431659	0.80[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[ASN][1000 genomes]
rs6737398	0.80[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[ASN][1000 genomes]
rs6754677	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs6861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7587633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7595748	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[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	nsv584699	chr2:234182240-234255547	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv584700	chr2:234199401-234364426	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6431262	ATG16L1	cis	cerebellum	SCAN
rs6431262	ATG16L1	cis	multi-tissue	Pritchard
rs6431262	ATG16L1	cis	brain	seeQTL
rs6431262	GIGYF2	cis	cerebellum	SCAN
rs6431262	SCARNA5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234162200-234205200	Strong transcription	HUES48 Cell Line	embryonic stem cell
2	chr2:234162200-234205200	Strong transcription	Fetal Muscle Trunk	muscle
3	chr2:234162400-234205200	Strong transcription	H1 Cell Line	embryonic stem cell
4	chr2:234162400-234205400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:234162600-234205000	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr2:234162600-234205200	Strong transcription	Fetal Muscle Leg	muscle
7	chr2:234162800-234205600	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:234163200-234206000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:234164200-234205400	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr2:234164200-234205400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:234164600-234206000	Strong transcription	HepG2	liver
12	chr2:234165000-234206000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr2:234165200-234205400	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr2:234166800-234206000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr2:234172200-234204800	Strong transcription	Placenta	Placenta
16	chr2:234176800-234207800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr2:234177000-234206000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr2:234177200-234205400	Strong transcription	Dnd41	blood
19	chr2:234178400-234205200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:234179000-234206200	Strong transcription	Fetal Thymus	thymus
21	chr2:234179200-234205600	Strong transcription	Fetal Brain Female	brain
22	chr2:234179600-234204000	Strong transcription	HUVEC	blood vessel
23	chr2:234179600-234205400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr2:234179600-234205400	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr2:234179600-234205600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr2:234179800-234205200	Strong transcription	Primary B cells from peripheral blood	blood
27	chr2:234180800-234206400	Strong transcription	Thymus	Thymus
28	chr2:234181000-234205200	Strong transcription	Liver	Liver
29	chr2:234181400-234216400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr2:234182400-234206000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr2:234183000-234204400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr2:234189200-234205200	Strong transcription	Brain Germinal Matrix	brain
33	chr2:234189200-234205400	Strong transcription	Duodenum Mucosa	Duodenum
34	chr2:234189200-234205600	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr2:234189600-234205200	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr2:234189800-234204600	Strong transcription	Placenta Amnion	Placenta Amnion
37	chr2:234189800-234205200	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr2:234190000-234205000	Strong transcription	Aorta	Aorta
39	chr2:234190000-234205600	Strong transcription	Fetal Intestine Small	intestine
40	chr2:234190200-234205400	Strong transcription	Spleen	Spleen
41	chr2:234190600-234205600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr2:234190600-234206600	Strong transcription	Fetal Stomach	stomach
43	chr2:234192000-234206000	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr2:234192400-234205000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr2:234193000-234205000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr2:234193000-234205000	Strong transcription	NHEK	skin
47	chr2:234193000-234205200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr2:234193000-234205200	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr2:234193000-234205200	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr2:234193000-234205400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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