Variant report

Variant	rs2930325
Chromosome Location	chr7:140415661-140415662
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:140414826..140417259-chr7:140419669..140421264,2	K562	blood:
2	chr7:140395317..140397215-chr7:140414761..140416702,2	K562	blood:
3	chr7:140414826..140417394-chr7:140419160..140421169,2	K562	blood:
4	chr7:140371637..140374196-chr7:140414800..140417349,2	MCF-7	breast:
5	chr7:140394913..140398367-chr7:140415393..140417213,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133597	Chromatin interaction
ENSG00000146966	Chromatin interaction
ENSG00000090266	Chromatin interaction
ENSG00000240889	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1106846	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11977567	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28828674	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2907951	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2907952	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2908235	0.88[EUR][1000 genomes]
rs2930315	1.00[CEU][hapmap]
rs2930316	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2930317	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2930320	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2930323	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2930326	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2930328	0.85[CEU][hapmap];1.00[CHD][hapmap]
rs2930329	0.85[CEU][hapmap];1.00[CHD][hapmap]
rs2930330	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2930332	0.86[EUR][1000 genomes]
rs2968546	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2968554	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2968556	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56347011	1.00[ASN][1000 genomes]
rs6969644	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6977496	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7785630	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7802537	0.85[CEU][hapmap];1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831157	chr7:140241339-140426876	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv3351231	chr7:140390303-140588539	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv831158	chr7:140392222-140602315	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv869260	chr7:140404835-140542905	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv1015269	chr7:140412464-140458821	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2930325	ADCK2	cis	Nerve Tibial	GTEx
rs2930325	MYBPC2	trans	lymphoblastoid	seeQTL
rs2930325	ADCK2	Cis_1M	lymphoblastoid	RTeQTL
rs2930325	ADCK2	cis	parietal	SCAN
rs2930325	TRIM24	cis	parietal	SCAN
rs2930325	MRPS33	cis	parietal	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140398000-140419400	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr7:140398000-140466600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr7:140398200-140473800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr7:140398200-140492600	Weak transcription	Colonic Mucosa	Colon
5	chr7:140398400-140422000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr7:140398400-140432200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr7:140398600-140459400	Weak transcription	Brain Germinal Matrix	brain
8	chr7:140398600-140491800	Weak transcription	Fetal Brain Male	brain
9	chr7:140399400-140468200	Weak transcription	Right Ventricle	heart
10	chr7:140399600-140443800	Weak transcription	Fetal Heart	heart
11	chr7:140400000-140474000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr7:140404400-140452400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr7:140404800-140419600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr7:140404800-140427600	Weak transcription	HSMMtube	muscle
15	chr7:140404800-140489000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr7:140404800-140517000	Weak transcription	Psoas Muscle	Psoas
17	chr7:140405200-140470800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr7:140405600-140472200	Weak transcription	Brain Substantia Nigra	brain
19	chr7:140406200-140418800	Weak transcription	Fetal Kidney	kidney
20	chr7:140406600-140472800	Weak transcription	Hela-S3	cervix
21	chr7:140407000-140425600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr7:140407000-140425600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr7:140407000-140427400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr7:140407000-140427600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr7:140407000-140428800	Weak transcription	NHLF	lung
26	chr7:140407000-140454200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr7:140407000-140466800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr7:140407200-140419000	Weak transcription	GM12878-XiMat	blood
29	chr7:140407200-140419200	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr7:140407200-140419400	Weak transcription	HUVEC	blood vessel
31	chr7:140407200-140419400	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr7:140407200-140419600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr7:140407200-140422000	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr7:140407200-140422400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr7:140407200-140424400	Weak transcription	Dnd41	blood
36	chr7:140407200-140424600	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr7:140407200-140424600	Weak transcription	Fetal Intestine Large	intestine
38	chr7:140407200-140425400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr7:140407200-140425400	Weak transcription	Brain Hippocampus Middle	brain
40	chr7:140407200-140425400	Weak transcription	Esophagus	oesophagus
41	chr7:140407200-140425400	Weak transcription	Stomach Smooth Muscle	stomach
42	chr7:140407200-140425400	Weak transcription	NH-A	brain
43	chr7:140407200-140425400	Weak transcription	NHEK	skin
44	chr7:140407200-140425400	Weak transcription	Osteobl	bone
45	chr7:140407200-140425600	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr7:140407200-140425600	Weak transcription	HSMM	muscle
47	chr7:140407200-140427600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr7:140407200-140427600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr7:140407200-140428000	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr7:140407200-140433600	Weak transcription	Adipose Nuclei	Adipose

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