Variant report

Variant	rs3912541
Chromosome Location	chr2:114725960-114725961
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:114718968..114721706-chr2:114724890..114726675,2	MCF-7	breast:
2	chr2:114719759..114722494-chr2:114725495..114728932,3	K562	blood:
3	chr2:114725172..114726759-chr2:114728569..114731437,2	K562	blood:
4	chr2:114719759..114724600-chr2:114725495..114731130,7	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11123212	0.94[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap]
rs12466636	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12478890	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12618768	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12711793	0.88[JPT][hapmap]
rs1566813	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1825738	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2046543	0.93[CEU][hapmap];0.82[AMR][1000 genomes]
rs275417	0.93[CEU][hapmap]
rs276318	0.81[AMR][1000 genomes]
rs276821	0.93[CEU][hapmap];0.89[MEX][hapmap];0.81[AMR][1000 genomes]
rs3748998	0.93[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3982221	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4341941	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4849297	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6542183	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6542185	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6705687	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72835432	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7595375	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7602093	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7606387	0.81[AMR][1000 genomes]
rs904498	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs974057	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv275040	chr2:114725846-114729087	Strong transcription Genic enhancers Weak transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3912541	SLC35F5	cis	cerebellum	SCAN
rs3912541	ZC3H8	cis	parietal	SCAN
rs3912541	DDX11L2	cis	Whole Blood	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114653600-114734800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:114668400-114735000	Weak transcription	Stomach Mucosa	stomach
3	chr2:114705200-114731200	Weak transcription	Lung	lung
4	chr2:114705200-114733000	Weak transcription	Pancreas	Pancrea
5	chr2:114705200-114734200	Weak transcription	Right Ventricle	heart
6	chr2:114705200-114736000	Weak transcription	Gastric	stomach
7	chr2:114705200-114737600	Weak transcription	Esophagus	oesophagus
8	chr2:114706200-114731400	Weak transcription	Aorta	Aorta
9	chr2:114706200-114731400	Weak transcription	Spleen	Spleen
10	chr2:114707400-114726800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:114709200-114731200	Weak transcription	Fetal Kidney	kidney
12	chr2:114710400-114728000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr2:114710400-114735800	Weak transcription	Colonic Mucosa	Colon
14	chr2:114710600-114727400	Weak transcription	Thymus	Thymus
15	chr2:114711200-114735400	Weak transcription	Fetal Lung	lung
16	chr2:114711800-114735400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr2:114713600-114732800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:114713800-114731400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:114713800-114732200	Weak transcription	Fetal Muscle Leg	muscle
20	chr2:114713800-114734600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr2:114713800-114735200	Weak transcription	Ovary	ovary
22	chr2:114713800-114736200	Weak transcription	Fetal Stomach	stomach
23	chr2:114714400-114735200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:114714800-114732800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:114715000-114744000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr2:114715200-114728400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr2:114715200-114735600	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr2:114715600-114732800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr2:114715600-114734800	Weak transcription	Left Ventricle	heart
30	chr2:114715600-114735400	Weak transcription	K562	blood
31	chr2:114715600-114737000	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr2:114716800-114729200	Weak transcription	Placenta	Placenta
33	chr2:114717600-114729400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr2:114718600-114726800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr2:114718600-114729000	Weak transcription	Fetal Thymus	thymus
36	chr2:114718600-114733000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr2:114718600-114735400	Weak transcription	Adipose Nuclei	Adipose
38	chr2:114718800-114728600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr2:114718800-114729000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr2:114718800-114743200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr2:114719200-114727600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr2:114719200-114728200	Weak transcription	GM12878-XiMat	blood
43	chr2:114719400-114727800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr2:114719400-114729200	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr2:114719400-114732400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr2:114719600-114729600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr2:114719800-114729200	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr2:114720000-114728600	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr2:114721000-114729200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr2:114721200-114729800	Weak transcription	HMEC	breast

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