Variant report

Variant	rs13009506
Chromosome Location	chr2:234175706-234175707
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:234174882..234177034-chr2:234181222..234183655,2	K562	blood:
2	chr2:234174620..234177065-chr2:234198174..234200296,2	MCF-7	breast:
3	chr2:234167721..234169330-chr2:234175113..234177265,2	K562	blood:

Variant related genes	Relation type
ENSG00000085978	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	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10165561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10167613	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10178603	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10186850	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10187752	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10187822	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10192579	0.81[ASN][1000 genomes]
rs10192702	0.85[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10195395	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10196794	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10199278	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10203952	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10206299	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10210302	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1045100	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.93[MKK][hapmap];0.83[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10929322	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10929325	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10929326	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11679791	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11680089	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11680130	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11687982	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11688431	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11690131	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11694081	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12162308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12692250	0.81[ASN][1000 genomes]
rs12692254	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12994971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12994997	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13003866	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13015823	0.82[JPT][hapmap]
rs13035837	0.83[JPT][hapmap]
rs13391356	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[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];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13412102	0.81[ASN][1000 genomes]
rs13418066	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1441092	0.83[JPT][hapmap]
rs1596017	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2119505	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2241878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2241879	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2241880	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289472	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289474	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289477	0.86[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs28454240	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2880080	0.96[CEU][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34123137	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34701569	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35300242	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36001488	0.92[AMR][1000 genomes];0.97[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	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792109	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816234	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828309	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55835501	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56049444	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56227616	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6431654	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]
rs6431660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6431661	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6705964	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6738490	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6745825	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6752107	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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]
rs7559194	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13009506	B3GNT7	cis	cerebellum	SCAN
rs13009506	SCARNA5	cis	parietal	SCAN
rs13009506	ATG16L1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234161800-234180600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:234162200-234205200	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr2:234162200-234205200	Strong transcription	Fetal Muscle Trunk	muscle
4	chr2:234162400-234192000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
5	chr2:234162400-234196400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:234162400-234205200	Strong transcription	H1 Cell Line	embryonic stem cell
7	chr2:234162400-234205400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:234162600-234176200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr2:234162600-234188600	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr2:234162600-234192400	Strong transcription	Osteobl	bone
11	chr2:234162600-234205000	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr2:234162600-234205200	Strong transcription	Fetal Muscle Leg	muscle
13	chr2:234162800-234194000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:234162800-234197000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr2:234162800-234205600	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr2:234163000-234176200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr2:234163000-234192200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr2:234163000-234192200	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr2:234163200-234177800	Strong transcription	NHEK	skin
20	chr2:234163200-234188000	Strong transcription	Stomach Smooth Muscle	stomach
21	chr2:234163200-234188800	Strong transcription	Duodenum Mucosa	Duodenum
22	chr2:234163200-234206000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:234163800-234188600	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr2:234163800-234189000	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr2:234164000-234177400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:234164200-234176800	Strong transcription	Fetal Brain Female	brain
27	chr2:234164200-234178800	Strong transcription	Fetal Lung	lung
28	chr2:234164200-234205400	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr2:234164200-234205400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:234164400-234192000	Strong transcription	NH-A	brain
31	chr2:234164400-234196800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr2:234164400-234197200	Strong transcription	Adipose Nuclei	Adipose
33	chr2:234164600-234176000	Strong transcription	Dnd41	blood
34	chr2:234164600-234176200	Strong transcription	HUVEC	blood vessel
35	chr2:234164600-234190400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr2:234164600-234192000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr2:234164600-234192200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:234164600-234206000	Strong transcription	HepG2	liver
39	chr2:234164800-234195800	Strong transcription	Fetal Intestine Large	intestine
40	chr2:234165000-234175800	Strong transcription	Primary B cells from cord blood	blood
41	chr2:234165000-234177000	Strong transcription	Left Ventricle	heart
42	chr2:234165000-234177200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr2:234165000-234192200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:234165000-234206000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr2:234165200-234177000	Strong transcription	Fetal Intestine Small	intestine
46	chr2:234165200-234182200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr2:234165200-234205400	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr2:234165400-234177000	Strong transcription	Fetal Stomach	stomach
49	chr2:234165400-234179400	Strong transcription	Rectal Smooth Muscle	rectum
50	chr2:234165400-234192000	Strong transcription	Brain Cingulate Gyrus	brain

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