Variant report

Variant	rs2473929
Chromosome Location	chr11:34174296-34174297
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:34159433..34161225-chr11:34173163..34174695,2	K562	blood:
2	chr11:34173802..34178236-chr11:34378169..34382437,4	MCF-7	breast:
3	chr11:34172563..34174315-chr11:34176884..34178666,2	MCF-7	breast:
4	chr11:34173254..34175718-chr11:34185959..34188757,2	K562	blood:
5	chr11:34098869..34100659-chr11:34172311..34174977,2	K562	blood:

Variant related genes	Relation type
ENSG00000166016	Chromatin interaction
ENSG00000135372	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10047428	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10047487	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10501132	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs10501133	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10836150	0.89[CEU][hapmap];0.91[GIH][hapmap];0.83[TSI][hapmap]
rs11552143	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16925114	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs16925115	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs16925121	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs16925126	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs16925134	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs16925147	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs16925153	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16925155	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs16925160	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16925163	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16925167	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16925170	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16925173	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16925175	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16925177	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16925181	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16925182	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16925183	1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap]
rs16925184	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16925219	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16926099	0.81[EUR][1000 genomes]
rs17367679	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17699090	0.81[EUR][1000 genomes]
rs17699505	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs17699517	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs17699883	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17700132	1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17700360	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17700714	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17700877	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17701015	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17771070	0.84[GIH][hapmap]
rs17771981	0.81[EUR][1000 genomes]
rs17777885	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs17777985	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs17778417	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17778759	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1883958	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2004272	0.81[EUR][1000 genomes]
rs2421456	0.81[EUR][1000 genomes]
rs2421457	0.81[EUR][1000 genomes]
rs2421459	0.89[CEU][hapmap];0.84[GIH][hapmap];0.83[TSI][hapmap]
rs2467392	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2467393	1.00[CEU][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2473932	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2957481	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2957509	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2957514	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2982587	0.94[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2982617	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2982619	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36117528	0.82[EUR][1000 genomes]
rs4074368	0.81[EUR][1000 genomes]
rs4237663	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4587708	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs4755357	0.83[EUR][1000 genomes]
rs4755359	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4756095	0.92[GIH][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs4756101	0.81[EUR][1000 genomes]
rs4756109	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs56693007	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56696374	0.84[EUR][1000 genomes]
rs56973150	0.84[EUR][1000 genomes]
rs57330513	0.84[EUR][1000 genomes]
rs57492451	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58755000	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59158919	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59249605	0.84[EUR][1000 genomes]
rs59359577	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59518134	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59650719	0.84[EUR][1000 genomes]
rs59972955	0.84[EUR][1000 genomes]
rs59978955	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs60015864	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60494596	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60549862	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60700110	0.84[EUR][1000 genomes]
rs61171154	0.84[EUR][1000 genomes]
rs6484694	0.82[EUR][1000 genomes]
rs7104352	0.90[CEU][hapmap]
rs7127581	0.81[EUR][1000 genomes]
rs73497050	0.81[EUR][1000 genomes]
rs73497064	0.81[EUR][1000 genomes]
rs73500434	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73501009	0.82[EUR][1000 genomes]
rs73501017	0.84[EUR][1000 genomes]
rs73501018	0.84[EUR][1000 genomes]
rs73501023	0.84[EUR][1000 genomes]
rs73501037	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73501038	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73501048	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73501059	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73501064	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73501065	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73501069	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73501097	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7483997	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7925527	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7933297	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7944654	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7951527	1.00[CEU][hapmap]
rs8191	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs958332	0.90[CEU][hapmap];0.81[EUR][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2473929	ABTB2	cis	parietal	SCAN
rs2473929	NBAS	trans	parietal	SCAN
rs2473929	NAT10	cis	parietal	SCAN
rs2473929	NAT10	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34128600-34176400	Strong transcription	Fetal Stomach	stomach
2	chr11:34128800-34178000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr11:34129000-34177400	Strong transcription	Osteobl	bone
4	chr11:34129000-34177800	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr11:34129200-34174600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr11:34129200-34177800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr11:34129400-34175600	Strong transcription	Fetal Thymus	thymus
8	chr11:34129600-34175000	Strong transcription	Brain Anterior Caudate	brain
9	chr11:34129600-34177200	Strong transcription	Skeletal Muscle Female	skeletal muscle
10	chr11:34129600-34178200	Strong transcription	Liver	Liver
11	chr11:34129800-34175000	Strong transcription	Primary T cells from cord blood	blood
12	chr11:34129800-34175000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr11:34129800-34175600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr11:34130000-34174600	Strong transcription	Dnd41	blood
15	chr11:34130000-34177000	Strong transcription	Sigmoid Colon	Sigmoid Colon
16	chr11:34130000-34181800	Strong transcription	A549	lung
17	chr11:34130200-34177600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr11:34136200-34177200	Strong transcription	Adipose Nuclei	Adipose
19	chr11:34136200-34177200	Strong transcription	Skeletal Muscle Male	skeletal muscle
20	chr11:34138800-34185600	Strong transcription	Fetal Brain Female	brain
21	chr11:34146200-34187600	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr11:34148000-34176200	Strong transcription	Brain Hippocampus Middle	brain
23	chr11:34150600-34175200	Strong transcription	Gastric	stomach
24	chr11:34150600-34178000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr11:34150800-34177200	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr11:34151800-34175400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr11:34152000-34175000	Strong transcription	Esophagus	oesophagus
28	chr11:34152000-34175000	Strong transcription	Stomach Smooth Muscle	stomach
29	chr11:34152200-34177600	Strong transcription	NHEK	skin
30	chr11:34152200-34184800	Strong transcription	Brain Germinal Matrix	brain
31	chr11:34152400-34186600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr11:34154600-34176800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
33	chr11:34155800-34177800	Strong transcription	Right Ventricle	heart
34	chr11:34157800-34176200	Strong transcription	H9 Cell Line	embryonic stem cell
35	chr11:34157800-34176200	Strong transcription	Thymus	Thymus
36	chr11:34164800-34177400	Strong transcription	Left Ventricle	heart
37	chr11:34165400-34177400	Weak transcription	Right Atrium	heart
38	chr11:34165800-34184600	Weak transcription	Stomach Mucosa	stomach
39	chr11:34166800-34182400	Weak transcription	Psoas Muscle	Psoas
40	chr11:34169600-34196200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr11:34170000-34174800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr11:34170200-34174400	Weak transcription	K562	blood
43	chr11:34170200-34175800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr11:34170200-34178600	Weak transcription	Small Intestine	intestine
45	chr11:34170200-34183400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr11:34170400-34176000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr11:34170400-34176600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr11:34170400-34177600	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr11:34170800-34182000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr11:34171000-34175800	Weak transcription	Rectal Smooth Muscle	rectum

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