Variant report

Variant	rs10165386
Chromosome Location	chr2:99301833-99301834
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99301026..99304352-chr2:99305405..99307955,3	K562	blood:
2	chr2:99299792..99302673-chr2:99315201..99317831,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10199926	0.95[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10207287	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10496329	0.88[CEU][hapmap]
rs12467276	0.88[CEU][hapmap]
rs12468086	0.92[CEU][hapmap]
rs17448085	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs17448190	0.81[EUR][1000 genomes]
rs17448211	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs17448420	0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs17514013	0.83[CEU][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs2309434	1.00[CEU][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs2871235	0.92[CEU][hapmap]
rs3769688	0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs3769689	0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs55633363	0.90[EUR][1000 genomes]
rs55646762	0.90[EUR][1000 genomes]
rs55730719	0.89[EUR][1000 genomes]
rs55859362	0.82[EUR][1000 genomes]
rs55939630	0.90[EUR][1000 genomes]
rs56027617	0.90[EUR][1000 genomes]
rs56070038	0.90[EUR][1000 genomes]
rs56163086	0.89[EUR][1000 genomes]
rs56305624	0.81[EUR][1000 genomes]
rs56354279	0.90[EUR][1000 genomes]
rs56371690	0.81[EUR][1000 genomes]
rs56375699	0.96[EUR][1000 genomes]
rs56945529	0.83[EUR][1000 genomes]
rs60889948	0.96[EUR][1000 genomes]
rs62157995	0.81[EUR][1000 genomes]
rs62157997	0.87[EUR][1000 genomes]
rs62157999	0.87[EUR][1000 genomes]
rs62158000	0.87[EUR][1000 genomes]
rs62158001	0.87[EUR][1000 genomes]
rs62158002	0.90[EUR][1000 genomes]
rs62158008	0.96[EUR][1000 genomes]
rs62158009	0.96[EUR][1000 genomes]
rs62158010	0.90[EUR][1000 genomes]
rs62158015	0.89[EUR][1000 genomes]
rs6742636	0.90[EUR][1000 genomes]
rs6742760	0.88[CEU][hapmap]
rs72825754	0.87[EUR][1000 genomes]
rs882164	0.92[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013941	chr2:99116255-99317933	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv535834	chr2:99116255-99317933	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv582516	chr2:99254031-99304794	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv2841	chr2:99296874-99342362	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10165386	MGAT4A	cis	multi-tissue	Pritchard

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99234600-99310600	Weak transcription	Small Intestine	intestine
2	chr2:99249800-99318000	Weak transcription	Psoas Muscle	Psoas
3	chr2:99251600-99302000	Weak transcription	Brain Angular Gyrus	brain
4	chr2:99251600-99306600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:99255600-99306800	Weak transcription	Colonic Mucosa	Colon
6	chr2:99265600-99306600	Weak transcription	Lung	lung
7	chr2:99265800-99303800	Weak transcription	Brain Substantia Nigra	brain
8	chr2:99266400-99304200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:99279200-99302200	Weak transcription	Right Ventricle	heart
10	chr2:99282800-99306600	Weak transcription	Left Ventricle	heart
11	chr2:99286800-99304800	Weak transcription	Gastric	stomach
12	chr2:99288000-99310000	Weak transcription	Thymus	Thymus
13	chr2:99291400-99302000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr2:99291600-99302200	Weak transcription	Liver	Liver
15	chr2:99291600-99302200	Weak transcription	Brain Anterior Caudate	brain
16	chr2:99291600-99302200	Weak transcription	Brain Hippocampus Middle	brain
17	chr2:99292000-99310400	Weak transcription	Primary B cells from peripheral blood	blood
18	chr2:99292200-99306600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr2:99292200-99312800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr2:99293400-99325200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr2:99293800-99302000	Weak transcription	HepG2	liver
22	chr2:99294000-99302000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr2:99294000-99304200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr2:99294200-99313600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr2:99294200-99315000	Weak transcription	Fetal Intestine Large	intestine
26	chr2:99294400-99315000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr2:99294400-99318600	Weak transcription	Spleen	Spleen
28	chr2:99294600-99306600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr2:99294600-99312600	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr2:99294600-99314200	Weak transcription	Fetal Intestine Small	intestine
31	chr2:99295000-99306000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr2:99295000-99325200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr2:99295200-99312600	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr2:99295600-99302400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr2:99295600-99310000	Weak transcription	Fetal Thymus	thymus
36	chr2:99295600-99310400	Weak transcription	Dnd41	blood
37	chr2:99298000-99302600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
38	chr2:99299600-99304200	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr2:99300000-99302200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr2:99300000-99315600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr2:99300400-99306800	Weak transcription	Stomach Smooth Muscle	stomach
42	chr2:99300600-99303600	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr2:99301200-99302200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr2:99301400-99302600	Genic enhancers	Primary T cells fromperipheralblood	blood
45	chr2:99301400-99302800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr2:99301400-99303200	Enhancers	Pancreas	Pancrea
47	chr2:99301600-99315800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr2:99301800-99302200	Enhancers	Primary T cells from cord blood	blood
49	chr2:99301800-99310400	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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