Variant report

Variant	rs61808940
Chromosome Location	chr1:169271020-169271021
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10442644	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12116551	0.81[EUR][1000 genomes]
rs12116683	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12117362	0.81[EUR][1000 genomes]
rs12117559	0.82[EUR][1000 genomes]
rs12117884	0.88[EUR][1000 genomes]
rs12118611	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12118645	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12120960	0.82[EUR][1000 genomes]
rs12121185	0.88[EUR][1000 genomes]
rs12121994	0.88[EUR][1000 genomes]
rs12122348	0.81[EUR][1000 genomes]
rs12124064	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12124738	0.80[EUR][1000 genomes]
rs12125057	0.81[EUR][1000 genomes]
rs12125501	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12129132	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12129567	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12130858	0.81[EUR][1000 genomes]
rs12142784	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12143193	0.88[EUR][1000 genomes]
rs12143790	0.81[EUR][1000 genomes]
rs12143963	0.81[EUR][1000 genomes]
rs12145146	0.88[EUR][1000 genomes]
rs12145193	0.81[EUR][1000 genomes]
rs12145226	0.88[EUR][1000 genomes]
rs12723917	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12728614	0.80[EUR][1000 genomes]
rs12731520	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12733626	0.87[EUR][1000 genomes]
rs12736817	0.81[EUR][1000 genomes]
rs12738167	0.88[EUR][1000 genomes]
rs12739337	0.87[EUR][1000 genomes]
rs12740501	0.81[EUR][1000 genomes]
rs12743588	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12744362	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12745978	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12750161	0.81[EUR][1000 genomes]
rs12751407	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12751571	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12753816	0.80[EUR][1000 genomes]
rs17349467	0.80[EUR][1000 genomes]
rs1936533	0.81[EUR][1000 genomes]
rs2040446	0.80[EUR][1000 genomes]
rs2157597	0.81[EUR][1000 genomes]
rs2420014	0.87[EUR][1000 genomes]
rs2420016	0.88[EUR][1000 genomes]
rs34176173	0.80[EUR][1000 genomes]
rs34248820	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34408435	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35091267	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35220898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35249110	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35271076	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35375125	0.87[EUR][1000 genomes]
rs35393101	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35447001	0.80[EUR][1000 genomes]
rs35458577	0.80[EUR][1000 genomes]
rs35539429	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36154866	0.87[EUR][1000 genomes]
rs3766090	0.88[EUR][1000 genomes]
rs4589164	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4656669	0.82[EUR][1000 genomes]
rs61806242	0.81[EUR][1000 genomes]
rs61806244	0.81[EUR][1000 genomes]
rs61806989	0.82[AFR][1000 genomes]
rs61808870	0.82[EUR][1000 genomes]
rs61808916	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71635617	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72700059	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7516097	0.81[EUR][1000 genomes]
rs7522781	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv429913	chr1:169177019-169296744	Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1010010	chr1:169189586-169347545	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv872531	chr1:169191860-169388193	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1012919	chr1:169200982-169324750	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1000254	chr1:169203554-169271792	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1004674	chr1:169233962-169271792	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs61808940	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs61808940	NME7	cis	Artery Tibial	GTEx
rs61808940	NME7	cis	Thyroid	GTEx
rs61808940	NME7	cis	Esophagus Muscularis	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169251400-169271400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:169252800-169278600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr1:169252800-169278800	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr1:169253600-169280600	Weak transcription	Fetal Kidney	kidney
5	chr1:169254000-169274800	Weak transcription	Ovary	ovary
6	chr1:169254800-169281000	Weak transcription	Dnd41	blood
7	chr1:169256800-169271600	Weak transcription	Primary B cells from cord blood	blood
8	chr1:169256800-169278600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr1:169257600-169284800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:169257800-169281200	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr1:169258600-169271200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:169258600-169276400	Weak transcription	HSMM	muscle
13	chr1:169258800-169274600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:169258800-169277400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:169259200-169278600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr1:169259400-169274800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr1:169259400-169278600	Weak transcription	Adipose Nuclei	Adipose
18	chr1:169259600-169278600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:169259600-169294400	Weak transcription	Pancreas	Pancrea
20	chr1:169260400-169310400	Weak transcription	Fetal Stomach	stomach
21	chr1:169260600-169278800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr1:169262400-169271400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:169262800-169274600	Weak transcription	Liver	Liver
24	chr1:169262800-169278600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr1:169263000-169278600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr1:169264000-169281400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:169264200-169278600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:169264400-169271600	Weak transcription	Psoas Muscle	Psoas
29	chr1:169264400-169294400	Weak transcription	Left Ventricle	heart
30	chr1:169265000-169278600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr1:169265000-169320400	Weak transcription	Aorta	Aorta
32	chr1:169265200-169272800	Weak transcription	HepG2	liver
33	chr1:169265200-169277200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:169265200-169278400	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr1:169265200-169281200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr1:169265400-169281200	Weak transcription	NHDF-Ad	bronchial
37	chr1:169265800-169281000	Weak transcription	Fetal Intestine Large	intestine
38	chr1:169266200-169278600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr1:169266200-169280200	Weak transcription	Fetal Muscle Leg	muscle
40	chr1:169267000-169278400	Weak transcription	Brain Anterior Caudate	brain
41	chr1:169267000-169281200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:169267800-169271400	Weak transcription	Primary T cells from cord blood	blood
43	chr1:169267800-169281200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:169268000-169278600	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr1:169268400-169271600	Weak transcription	Fetal Brain Male	brain
46	chr1:169269000-169278800	Weak transcription	Fetal Brain Female	brain
47	chr1:169269000-169281200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:169269200-169281400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr1:169269400-169271400	Weak transcription	Primary hematopoietic stem cells	blood
50	chr1:169269400-169271600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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