Variant report

Variant	rs7349405
Chromosome Location	chr2:55391294-55391295
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55279956..55282350-chr2:55389384..55392221,3	K562	blood:
2	chr2:55275064..55280479-chr2:55390367..55395295,9	MCF-7	breast:
3	chr2:55334946..55336599-chr2:55390126..55391859,2	MCF-7	breast:
4	chr2:55391168..55392772-chr2:55394267..55395800,2	MCF-7	breast:
5	chr2:55389326..55391363-chr2:55393207..55395340,2	K562	blood:
6	chr2:55273759..55277470-chr2:55389795..55392112,3	K562	blood:
7	chr2:55274543..55277923-chr2:55387934..55394752,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction
ENSG00000266376	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs17046778	0.84[ASN][1000 genomes]
rs1821832	0.81[AMR][1000 genomes]
rs2576722	0.90[CHB][hapmap];0.83[AMR][1000 genomes]
rs2589069	1.00[YRI][hapmap]
rs34348115	0.89[CHD][hapmap];0.93[MEX][hapmap]
rs4435493	0.86[CHD][hapmap]
rs57681837	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59439819	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59783675	0.90[AMR][1000 genomes]
rs61109509	0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs61486882	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6726380	0.81[ASN][1000 genomes]
rs7349360	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7568777	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs934709	0.88[CHD][hapmap]

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	nsv1010438	chr2:55373562-55450144	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs7349405	CLHC1	cis	Stomach	GTEx
rs7349405	CLHC1	cis	Esophagus Muscularis	GTEx
rs7349405	VRK2	cis	parietal	SCAN
rs7349405	CLHC1	cis	Nerve Tibial	GTEx
rs7349405	CLHC1	cis	Artery Aorta	GTEx
rs7349405	CLHC1	cis	lung	GTEx
rs7349405	CLHC1	cis	Artery Tibial	GTEx
rs7349405	CLHC1	cis	Adipose Subcutaneous	GTEx
rs7349405	C2orf63	cis	lymphoblastoid	seeQTL
rs7349405	CLHC1	cis	Heart Left Ventricle	GTEx
rs7349405	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL
rs7349405	AC012358.7	cis	Adipose Subcutaneous	GTEx
rs7349405	CLHC1	cis	Esophagus Mucosa	GTEx
rs7349405	LOC388720///RPS27A	Cis_1M	lymphoblastoid	RTeQTL
rs7349405	FLJ31438	cis	multi-tissue	Pritchard
rs7349405	C2orf63	cis	multi-tissue	Pritchard
rs7349405	CLHC1	cis	Whole Blood	GTEx
rs7349405	CLHC1	cis	Muscle Skeletal	GTEx
rs7349405	CLHC1	cis	Thyroid	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55383600-55395600	Enhancers	Pancreas	Pancrea
2	chr2:55384000-55392800	Weak transcription	HMEC	breast
3	chr2:55384800-55392200	Weak transcription	Right Ventricle	heart
4	chr2:55386000-55395000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:55386800-55416600	Weak transcription	Esophagus	oesophagus
6	chr2:55387400-55393800	Weak transcription	Fetal Heart	heart
7	chr2:55387400-55395600	Enhancers	Lung	lung
8	chr2:55387600-55395000	Weak transcription	Psoas Muscle	Psoas
9	chr2:55387800-55392400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr2:55388000-55395200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:55388400-55392000	Enhancers	Fetal Brain Male	brain
12	chr2:55388400-55392200	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr2:55388600-55392000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:55388600-55392400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:55388600-55393200	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr2:55388600-55393400	Enhancers	NH-A	brain
17	chr2:55388800-55391600	Enhancers	Fetal Brain Female	brain
18	chr2:55388800-55391600	Enhancers	Gastric	stomach
19	chr2:55388800-55392200	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr2:55388800-55392400	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr2:55388800-55395000	Weak transcription	Left Ventricle	heart
22	chr2:55389000-55394800	Enhancers	Brain Cingulate Gyrus	brain
23	chr2:55389000-55394800	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr2:55389200-55393200	Enhancers	HUVEC	blood vessel
25	chr2:55389200-55394000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:55389200-55394800	Enhancers	Brain Anterior Caudate	brain
27	chr2:55389200-55397400	Enhancers	NHLF	lung
28	chr2:55389400-55391600	Enhancers	HSMM	muscle
29	chr2:55389400-55394800	Enhancers	Brain Hippocampus Middle	brain
30	chr2:55389400-55395200	Weak transcription	NHEK	skin
31	chr2:55389600-55392000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
32	chr2:55389600-55392400	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr2:55389800-55391600	Enhancers	Placenta	Placenta
34	chr2:55389800-55392000	Enhancers	Fetal Lung	lung
35	chr2:55389800-55394000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr2:55389800-55394600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:55389800-55395000	Weak transcription	Brain Germinal Matrix	brain
38	chr2:55389800-55396000	Enhancers	Fetal Muscle Leg	muscle
39	chr2:55390000-55391400	Enhancers	Rectal Smooth Muscle	rectum
40	chr2:55390000-55391400	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr2:55390000-55393000	Enhancers	Colon Smooth Muscle	Colon
42	chr2:55390000-55393400	Enhancers	Fetal Kidney	kidney
43	chr2:55390000-55393600	Enhancers	Osteobl	bone
44	chr2:55390000-55393800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr2:55390000-55395600	Enhancers	Ovary	ovary
46	chr2:55390200-55392800	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr2:55390200-55393000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:55390200-55394800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr2:55390200-55395200	Weak transcription	Primary hematopoietic stem cells	blood
50	chr2:55390400-55391400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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