Variant report

Variant	rs6431654
Chromosome Location	chr2:234161769-234161770
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:234161754..234164546-chr2:234176635..234178201,2	K562	blood:
2	chr2:234160919..234163001-chr2:234739570..234741620,2	MCF-7	breast:
3	chr2:234161693..234166047-chr2:234167019..234170688,4	MCF-7	breast:
4	chr2:234161380..234162946-chr2:234262320..234263991,2	MCF-7	breast:
5	chr2:234161285..234164496-chr2:234179412..234182858,4	MCF-7	breast:
6	chr2:234161323..234164097-chr2:234164693..234167813,4	K562	blood:

Variant related genes	Relation type
ENSG00000077044	Chromatin interaction
ENSG00000243637	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10164737	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10165561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10167613	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10178603	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10186850	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10187752	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10187822	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10192579	0.81[ASN][1000 genomes]
rs10192702	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10195395	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10196794	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10199278	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10203952	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10206299	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10210302	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1045100	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10929322	0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10929325	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10929326	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11679791	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11680089	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11680130	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11687982	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11688431	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11690131	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11694081	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12162308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12692250	0.81[ASN][1000 genomes]
rs12692254	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12994971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12994997	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13003866	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13009506	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13015823	0.82[JPT][hapmap]
rs13035837	0.83[JPT][hapmap]
rs13391356	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13411660	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13412102	0.81[ASN][1000 genomes]
rs13418066	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1441092	0.83[JPT][hapmap]
rs1596017	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2119505	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2241878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2241879	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2241880	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289472	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289474	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289477	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap]
rs28454240	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2880080	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34123137	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34701569	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35300242	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36001488	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762588	0.83[JPT][hapmap]
rs3792106	0.95[CHB][hapmap];0.80[MEX][hapmap];0.84[ASN][1000 genomes]
rs3792108	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792109	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816234	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828309	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55835501	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56049444	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56227616	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6431660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6431661	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6705964	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6738490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6745825	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6752107	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[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];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7559194	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6431654	ATG16L1	cis	cerebellum	SCAN
rs6431654	B3GNT7	cis	cerebellum	SCAN
rs6431654	SCARNA5	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234159800-234161800	Active TSS	H9 Cell Line	embryonic stem cell
2	chr2:234159800-234161800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:234159800-234161800	Active TSS	Fetal Intestine Large	intestine
4	chr2:234159800-234161800	Active TSS	Psoas Muscle	Psoas
5	chr2:234160000-234161800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:234160000-234163800	Active TSS	GM12878-XiMat	blood
7	chr2:234160200-234161800	Active TSS	H1 Cell Line	embryonic stem cell
8	chr2:234160200-234161800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr2:234160200-234162000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:234160400-234161800	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr2:234160800-234161800	Flanking Active TSS	Primary hematopoietic stem cells	blood
12	chr2:234160800-234161800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:234160800-234161800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr2:234160800-234161800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
15	chr2:234160800-234161800	Flanking Active TSS	Brain Angular Gyrus	brain
16	chr2:234160800-234161800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr2:234160800-234162000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:234161000-234161800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:234161000-234161800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr2:234161000-234161800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr2:234161000-234161800	Flanking Active TSS	Liver	Liver
22	chr2:234161000-234161800	Flanking Active TSS	Brain Cingulate Gyrus	brain
23	chr2:234161000-234161800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr2:234161000-234162000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:234161000-234162000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
26	chr2:234161000-234162000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
27	chr2:234161000-234163000	Enhancers	Fetal Heart	heart
28	chr2:234161200-234161800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr2:234161200-234161800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr2:234161200-234161800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr2:234161200-234161800	Flanking Active TSS	Stomach Smooth Muscle	stomach
32	chr2:234161200-234161800	Flanking Active TSS	Thymus	Thymus
33	chr2:234161200-234161800	Flanking Active TSS	HUVEC	blood vessel
34	chr2:234161200-234162000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr2:234161200-234162000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr2:234161200-234162000	Flanking Active TSS	Brain Anterior Caudate	brain
37	chr2:234161200-234162000	Flanking Active TSS	Duodenum Mucosa	Duodenum
38	chr2:234161200-234162000	Flanking Active TSS	Fetal Brain Female	brain
39	chr2:234161200-234162000	Flanking Active TSS	Fetal Lung	lung
40	chr2:234161200-234162000	Enhancers	Small Intestine	intestine
41	chr2:234161200-234162400	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr2:234161200-234162400	Enhancers	Fetal Brain Male	brain
43	chr2:234161200-234163200	Enhancers	Spleen	Spleen
44	chr2:234161400-234161800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:234161400-234161800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr2:234161400-234161800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr2:234161400-234161800	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
48	chr2:234161400-234161800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
49	chr2:234161400-234161800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
50	chr2:234161400-234161800	Flanking Active TSS	Brain Germinal Matrix	brain

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