Variant report

Variant	rs2973444
Chromosome Location	chr5:90417593-90417594
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:90413771..90418676-chr5:90419460..90425678,7	K562	blood:
2	chr5:90414268..90417626-chr5:90676737..90680178,4	K562	blood:
3	chr5:90415624..90418676-chr5:90421411..90423997,3	K562	blood:
4	chr5:90414268..90419029-chr5:90677575..90681410,6	K562	blood:

Variant related genes	Relation type
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12109264	0.88[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs16869403	0.84[YRI][hapmap]
rs16869425	0.90[CEU][hapmap];0.94[YRI][hapmap]
rs1828177	0.84[YRI][hapmap]
rs1828178	0.83[YRI][hapmap]
rs1852731	0.90[CEU][hapmap]
rs1986718	0.90[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2367182	1.00[CHB][hapmap]
rs2950849	0.90[CEU][hapmap]
rs2950850	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2950851	0.90[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2950852	0.81[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2950853	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2950854	0.90[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2950855	0.90[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2973445	0.90[CEU][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2973447	0.90[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2973448	0.88[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2973449	0.90[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2973450	0.90[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2973453	0.90[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2973454	0.90[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2973455	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2973456	0.90[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs3112484	0.90[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs3114655	1.00[CHB][hapmap]
rs3952745	0.90[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs56377639	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs59654682	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs60689150	1.00[ASN][1000 genomes]
rs689544	0.81[YRI][hapmap]
rs73187188	1.00[ASN][1000 genomes]
rs73189003	1.00[ASN][1000 genomes]
rs73189008	0.85[AMR][1000 genomes]
rs949788	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024813	chr5:90321535-90870739	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv537806	chr5:90321535-90870739	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2973444	TMEM14C	trans	lymphoblastoid	RTeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90396200-90422800	Weak transcription	Esophagus	oesophagus
2	chr5:90401600-90431800	Weak transcription	K562	blood
3	chr5:90403000-90431600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr5:90403200-90431600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:90403400-90418800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr5:90403400-90418800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr5:90406600-90421800	Weak transcription	Small Intestine	intestine
8	chr5:90406800-90418600	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr5:90409200-90418400	Weak transcription	Fetal Brain Female	brain
10	chr5:90410800-90419200	Weak transcription	Brain Anterior Caudate	brain
11	chr5:90411000-90421600	Weak transcription	Brain Hippocampus Middle	brain
12	chr5:90414000-90420000	Enhancers	NHDF-Ad	bronchial
13	chr5:90414600-90418400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr5:90414600-90419000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr5:90414800-90418600	Weak transcription	NHLF	lung
16	chr5:90414800-90420600	Enhancers	Stomach Smooth Muscle	stomach
17	chr5:90415000-90421800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr5:90415400-90418600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr5:90415400-90418800	Weak transcription	Psoas Muscle	Psoas
20	chr5:90415400-90419600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr5:90415400-90419600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr5:90415400-90422600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr5:90415600-90419800	Enhancers	Adipose Nuclei	Adipose
24	chr5:90415600-90422000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr5:90415800-90418200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:90415800-90418600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr5:90416000-90418400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr5:90416000-90418600	Weak transcription	Ovary	ovary
29	chr5:90416000-90418600	Weak transcription	Right Atrium	heart
30	chr5:90416000-90420800	Weak transcription	Left Ventricle	heart
31	chr5:90416000-90420800	Weak transcription	Pancreas	Pancrea
32	chr5:90416000-90422200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr5:90416000-90422600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr5:90416000-90422600	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr5:90416000-90430000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr5:90416200-90418200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr5:90416200-90421600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr5:90416200-90421800	Weak transcription	Stomach Mucosa	stomach
39	chr5:90416400-90418800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr5:90416600-90417800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr5:90416600-90418800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:90416600-90419200	Weak transcription	Aorta	Aorta
43	chr5:90416600-90421600	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr5:90416600-90421800	Weak transcription	Fetal Stomach	stomach
45	chr5:90416600-90422200	Weak transcription	Fetal Muscle Leg	muscle
46	chr5:90416600-90422600	Weak transcription	Lung	lung
47	chr5:90416800-90418400	Weak transcription	Fetal Lung	lung
48	chr5:90416800-90418600	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr5:90416800-90421000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr5:90417000-90418000	Enhancers	HMEC	breast

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