Variant report

Variant	rs3884241
Chromosome Location	chr3:138233904-138233905
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10804658	0.80[CEU][hapmap]
rs10935282	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11709290	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11916525	0.82[JPT][hapmap]
rs12490633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs12630060	0.82[JPT][hapmap]
rs12632794	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs12635490	0.87[JPT][hapmap]
rs12635904	0.82[JPT][hapmap]
rs12636246	0.81[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs12636910	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12637679	0.83[JPT][hapmap]
rs13059817	0.83[JPT][hapmap]
rs13062423	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs13084780	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs13098554	0.83[JPT][hapmap]
rs1379257	0.89[CEU][hapmap]
rs1563615	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs1672927	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1672928	0.85[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap]
rs1672932	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs1673607	0.89[CEU][hapmap]
rs1673608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1673622	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1679167	0.82[CEU][hapmap]
rs1679169	0.93[YRI][hapmap]
rs2607795	0.89[CEU][hapmap]
rs2881793	0.89[CEU][hapmap]
rs361076	0.80[CEU][hapmap]
rs3813264	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3884240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs497334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs503922	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs529615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs542010	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs550507	0.90[CEU][hapmap]
rs559313	0.89[CEU][hapmap]
rs564800	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs586946	0.90[CEU][hapmap]
rs609797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs611134	0.89[CEU][hapmap]
rs629884	0.89[CEU][hapmap]
rs6439809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6439810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6763380	0.86[CEU][hapmap]
rs680070	0.90[CEU][hapmap]
rs7625326	0.90[CEU][hapmap]
rs7626226	1.00[CEU][hapmap]
rs7627685	0.89[CEU][hapmap]
rs7634745	0.89[CEU][hapmap]
rs7643973	0.89[CEU][hapmap]
rs7645920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs7653815	0.89[CEU][hapmap]
rs773444	0.90[CEU][hapmap]
rs773450	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs774012	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs814022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9049	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs936316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9811052	0.89[CEU][hapmap]
rs9817419	0.89[CEU][hapmap]
rs9848718	0.89[CEU][hapmap]
rs9848938	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs9855306	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	esv3447663	chr3:138096329-138273034	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv999041	chr3:138148812-138347988	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv522517	chr3:138174523-138297982	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1013074	chr3:138213166-138737688	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv1002612	chr3:138213274-138831792	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv536726	chr3:138213274-138831792	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv877538	chr3:138218709-138311201	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1009726	chr3:138219923-138737688	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	nsv877539	chr3:138224220-138261288	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3884241	FAIM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138194000-138260200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:138209400-138236800	Weak transcription	Aorta	Aorta
3	chr3:138209800-138258600	Weak transcription	Primary T cells from cord blood	blood
4	chr3:138210400-138236800	Weak transcription	Brain Substantia Nigra	brain
5	chr3:138210400-138242000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr3:138210800-138260600	Weak transcription	Colonic Mucosa	Colon
7	chr3:138211000-138236600	Weak transcription	Spleen	Spleen
8	chr3:138211200-138260600	Weak transcription	Brain Angular Gyrus	brain
9	chr3:138211800-138260600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr3:138212000-138235000	Weak transcription	Brain Germinal Matrix	brain
11	chr3:138212000-138235800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr3:138212400-138236600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:138212400-138236600	Weak transcription	Esophagus	oesophagus
14	chr3:138212600-138236600	Weak transcription	Lung	lung
15	chr3:138212600-138250200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:138212800-138236800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:138212800-138249800	Weak transcription	Small Intestine	intestine
18	chr3:138213200-138236600	Weak transcription	Ovary	ovary
19	chr3:138213200-138236600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr3:138213200-138243800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr3:138214200-138236600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:138214400-138260600	Weak transcription	Right Ventricle	heart
23	chr3:138215600-138236400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr3:138215800-138236600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:138216000-138235800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr3:138216600-138239400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr3:138217000-138236000	Weak transcription	Fetal Intestine Large	intestine
28	chr3:138217000-138237600	Weak transcription	Fetal Kidney	kidney
29	chr3:138218200-138239600	Weak transcription	Fetal Brain Female	brain
30	chr3:138218600-138254000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:138219000-138234600	Weak transcription	Dnd41	blood
32	chr3:138219000-138235200	Weak transcription	Fetal Stomach	stomach
33	chr3:138219000-138235600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:138219000-138235800	Weak transcription	Fetal Muscle Leg	muscle
35	chr3:138219000-138236200	Weak transcription	Fetal Intestine Small	intestine
36	chr3:138219000-138236200	Weak transcription	Thymus	Thymus
37	chr3:138219000-138236600	Weak transcription	Gastric	stomach
38	chr3:138219000-138236800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr3:138219000-138247000	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr3:138219400-138263200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr3:138223800-138234800	Weak transcription	Fetal Lung	lung
42	chr3:138224600-138234400	Weak transcription	Primary hematopoietic stem cells	blood
43	chr3:138225200-138236800	Weak transcription	Fetal Muscle Trunk	muscle
44	chr3:138225400-138259600	Weak transcription	Brain Anterior Caudate	brain
45	chr3:138227200-138236800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr3:138227400-138236600	Weak transcription	Adipose Nuclei	Adipose
47	chr3:138228400-138234600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:138228400-138236800	Weak transcription	Pancreas	Pancrea
49	chr3:138228800-138234800	Weak transcription	Duodenum Mucosa	Duodenum
50	chr3:138228800-138235400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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