Variant report

Variant	rs4670938
Chromosome Location	chr2:39680389-39680390
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39676819..39680637-chr2:39680981..39683418,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM178-4	chr2:39680010-39680916	l_1814_chr2:39518006-39558253_76bGuttman_hLF

Variant related genes	Relation type
ENSG00000231312	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10169501	0.81[ASN][1000 genomes]
rs10173722	0.80[ASN][1000 genomes]
rs10196447	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs10199459	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10199948	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs11124683	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11896389	0.97[EUR][1000 genomes]
rs12328714	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12624242	0.85[MKK][hapmap]
rs12712640	0.89[MKK][hapmap]
rs17023530	0.88[EUR][1000 genomes]
rs17023542	0.82[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs17023547	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs17023600	0.88[EUR][1000 genomes]
rs17023611	0.88[EUR][1000 genomes]
rs17023684	0.94[EUR][1000 genomes]
rs17023696	0.82[CEU][hapmap];0.90[GIH][hapmap];0.94[EUR][1000 genomes]
rs17023773	0.91[EUR][1000 genomes]
rs17446102	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs17446515	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs17446690	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs17505580	0.88[EUR][1000 genomes]
rs17505877	0.88[EUR][1000 genomes]
rs2056653	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2056655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2111383	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2373530	1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap]
rs2373532	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3732052	0.94[EUR][1000 genomes]
rs4670273	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55761128	0.94[EUR][1000 genomes]
rs6544227	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6544229	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6720537	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6720951	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6721049	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6721740	0.91[EUR][1000 genomes]
rs6731310	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6758596	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73924009	0.94[EUR][1000 genomes]
rs7559436	0.94[EUR][1000 genomes]
rs7577097	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7588265	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7596222	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7605939	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv2695	chr2:39643221-39688015	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv215442	chr2:39676634-39681883	Strong transcription Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39665200-39696000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:39665600-39681600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:39665600-39684200	Weak transcription	Lung	lung
4	chr2:39665600-39685600	Weak transcription	Left Ventricle	heart
5	chr2:39665600-39694600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:39665600-39694800	Weak transcription	Pancreas	Pancrea
7	chr2:39666000-39681200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr2:39666200-39681400	Weak transcription	Fetal Intestine Large	intestine
9	chr2:39666200-39696600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:39666600-39682200	Weak transcription	Fetal Muscle Leg	muscle
11	chr2:39666800-39681000	Weak transcription	Brain Substantia Nigra	brain
12	chr2:39666800-39681600	Weak transcription	Ovary	ovary
13	chr2:39667000-39681400	Weak transcription	Duodenum Mucosa	Duodenum
14	chr2:39667000-39681600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr2:39667000-39694600	Weak transcription	HSMMtube	muscle
16	chr2:39667200-39685200	Weak transcription	NHEK	skin
17	chr2:39667200-39694600	Weak transcription	NHLF	lung
18	chr2:39667200-39694800	Weak transcription	Brain Angular Gyrus	brain
19	chr2:39667200-39696400	Weak transcription	Fetal Heart	heart
20	chr2:39667400-39682000	Weak transcription	HSMM	muscle
21	chr2:39667400-39694600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr2:39667400-39694600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr2:39668200-39681400	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr2:39668200-39684800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr2:39668200-39685000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:39668200-39694800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr2:39668200-39696800	Weak transcription	Right Ventricle	heart
28	chr2:39670400-39682800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr2:39670400-39685000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr2:39670800-39684800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:39671000-39682200	Weak transcription	Primary hematopoietic stem cells	blood
32	chr2:39671200-39681200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr2:39671200-39685000	Weak transcription	Aorta	Aorta
34	chr2:39671600-39682600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:39671800-39682000	Weak transcription	Brain Cingulate Gyrus	brain
36	chr2:39672000-39681400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr2:39672200-39681400	Weak transcription	Adipose Nuclei	Adipose
38	chr2:39672200-39684600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:39672600-39681400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr2:39673400-39681000	Weak transcription	Liver	Liver
41	chr2:39673600-39681000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr2:39675000-39696400	Weak transcription	Fetal Kidney	kidney
43	chr2:39675200-39680800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr2:39675200-39682600	Weak transcription	Osteobl	bone
45	chr2:39675200-39682800	Weak transcription	HMEC	breast
46	chr2:39675200-39686000	Weak transcription	NHDF-Ad	bronchial
47	chr2:39675400-39682200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr2:39675400-39694600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr2:39675600-39682400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr2:39676000-39684800	Weak transcription	Fetal Intestine Small	intestine

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