Variant report

Variant	rs4606978
Chromosome Location	chr2:48643436-48643437
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:48336673..48339163-chr2:48642028..48644836,2	K562	blood:
2	chr2:48641901..48644739-chr2:48646186..48647771,2	K562	blood:
3	chr2:48540493..48542753-chr2:48643021..48644548,2	K562	blood:

Variant related genes	Relation type
ENSG00000170802	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10208627	0.84[ASN][1000 genomes]
rs10211336	0.92[ASN][1000 genomes]
rs10454133	1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10454134	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10495951	0.83[JPT][hapmap]
rs10495952	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs11679523	0.83[JPT][hapmap]
rs11680719	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs11680916	0.82[JPT][hapmap]
rs11683639	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs11683708	0.92[ASN][1000 genomes]
rs11685861	0.83[JPT][hapmap]
rs11688481	0.84[CHD][hapmap];0.83[JPT][hapmap]
rs11689622	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs11690690	0.83[JPT][hapmap]
rs11690748	0.83[JPT][hapmap]
rs11690845	0.83[JPT][hapmap]
rs12105983	0.84[ASN][1000 genomes]
rs13399936	0.96[ASN][1000 genomes]
rs13400909	0.95[ASN][1000 genomes]
rs13401749	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs13401752	0.95[ASN][1000 genomes]
rs13429377	0.83[AFR][1000 genomes]
rs17037289	0.84[CHD][hapmap];0.83[JPT][hapmap]
rs17037298	0.83[JPT][hapmap]
rs17855177	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs4267555	0.82[JPT][hapmap]
rs4274640	0.95[ASN][1000 genomes]
rs4316980	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4344965	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs4438532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4494796	0.97[ASN][1000 genomes]
rs4638844	0.89[ASN][1000 genomes]
rs4641990	0.84[CEU][hapmap]
rs55640438	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55757090	0.89[ASN][1000 genomes]
rs55971719	0.90[ASN][1000 genomes]
rs56365822	0.88[ASN][1000 genomes]
rs58020097	0.95[ASN][1000 genomes]
rs58969359	0.95[ASN][1000 genomes]
rs58978223	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59045263	0.84[ASN][1000 genomes]
rs60042255	0.88[ASN][1000 genomes]
rs60988618	0.94[ASN][1000 genomes]
rs61303367	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62137018	0.90[ASN][1000 genomes]
rs62137019	0.93[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs62137021	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62137041	0.97[ASN][1000 genomes]
rs66705539	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6705802	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs6718068	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs6732196	0.97[ASN][1000 genomes]
rs6735288	0.84[ASN][1000 genomes]
rs6743757	0.82[JPT][hapmap]
rs6747441	0.87[ASN][1000 genomes]
rs6749773	0.88[ASN][1000 genomes]
rs72820454	0.88[ASN][1000 genomes]
rs72820474	0.99[ASN][1000 genomes]
rs72820479	0.97[ASN][1000 genomes]
rs72820484	0.96[ASN][1000 genomes]
rs72820492	0.94[ASN][1000 genomes]
rs72820494	0.95[ASN][1000 genomes]
rs72820499	0.94[ASN][1000 genomes]
rs7562069	0.83[JPT][hapmap]
rs7562816	0.83[JPT][hapmap]
rs7565792	0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs7566239	0.83[JPT][hapmap]
rs7568574	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7576964	0.81[CHD][hapmap]
rs7577237	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs7579932	0.82[JPT][hapmap]
rs7600794	0.83[JPT][hapmap]
rs7606104	0.83[JPT][hapmap]

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	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv581775	chr2:48619869-48714938	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv518718	chr2:48624007-48650308	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4606978	CCDC128	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48639600-48645200	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr2:48639600-48647400	Enhancers	Liver	Liver
3	chr2:48640000-48643600	Enhancers	Fetal Intestine Large	intestine
4	chr2:48640000-48646200	Enhancers	Fetal Intestine Small	intestine
5	chr2:48640400-48647600	Weak transcription	Colon Smooth Muscle	Colon
6	chr2:48640400-48647600	Weak transcription	Ovary	ovary
7	chr2:48640600-48647800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr2:48641000-48647400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr2:48641400-48643600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:48641400-48643800	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr2:48641800-48643600	Enhancers	Primary hematopoietic stem cells	blood
12	chr2:48641800-48643800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:48641800-48643800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:48641800-48643800	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr2:48641800-48643800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr2:48641800-48643800	Enhancers	Fetal Brain Female	brain
17	chr2:48641800-48643800	Flanking Active TSS	HepG2	liver
18	chr2:48641800-48643800	Enhancers	HSMMtube	muscle
19	chr2:48641800-48644000	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr2:48642000-48643600	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr2:48642000-48643600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:48642000-48643600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr2:48642000-48643600	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr2:48642000-48643600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:48642000-48643600	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr2:48642000-48643600	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr2:48642000-48643600	Enhancers	Rectal Mucosa Donor 29	rectum
28	chr2:48642000-48643600	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr2:48642000-48643600	Enhancers	Dnd41	blood
30	chr2:48642000-48643600	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr2:48642000-48643600	Enhancers	NHDF-Ad	bronchial
32	chr2:48642000-48643800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr2:48642000-48643800	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr2:48642000-48643800	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr2:48642200-48643600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
36	chr2:48642200-48643600	Enhancers	H1 Cell Line	embryonic stem cell
37	chr2:48642200-48643600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:48642200-48643600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:48642200-48643600	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr2:48642200-48643600	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr2:48642200-48643600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:48642200-48643600	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr2:48642200-48643600	Enhancers	Primary B cells from peripheral blood	blood
44	chr2:48642200-48643600	Enhancers	Primary T cells fromperipheralblood	blood
45	chr2:48642200-48643600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr2:48642200-48643600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr2:48642200-48643600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr2:48642200-48643600	Enhancers	Fetal Brain Male	brain
49	chr2:48642200-48643600	Enhancers	Fetal Lung	lung
50	chr2:48642200-48643600	Enhancers	Fetal Muscle Trunk	muscle

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