Variant report

Variant	rs2930320
Chromosome Location	chr7:140375762-140375763
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr7:140375440-140376498	GM12878	blood:	n/a	n/a
2	SMC3	chr7:140374979-140375917	SK-N-SH	brain:	n/a	n/a
3	MTA3	chr7:140375695-140376626	GM12878	blood:	n/a	n/a
4	BRCA1	chr7:140375747-140375848	Hela-S3	cervix:	n/a	n/a
5	SPI1	chr7:140375696-140376931	GM12878	blood:	n/a	chr7:140376301-140376310 chr7:140376297-140376306
6	JUN	chr7:140374791-140375957	K562	blood:	n/a	n/a
7	CTCF	chr7:140374862-140375788	SK-N-SH	brain:	n/a	n/a
8	RAD21	chr7:140374883-140376639	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:140370608..140383131-chr7:140387718..140398587,28	MCF-7	breast:
2	chr7:140371506..140376729-chr7:140377280..140380130,6	K562	blood:
3	chr7:140374747..140377126-chr7:140623652..140625278,2	K562	blood:
4	chr7:140374979..140375913-chr7:140711999..140712535,2	MCF-7	breast:
5	chr7:140375224..140375862-chr7:140711603..140712374,2	K562	blood:

Variant related genes	Relation type
ADCK2	TF binding region
DENND2A	TF binding region
ENSG00000157764	Chromatin interaction
ENSG00000090266	Chromatin interaction
ENSG00000133597	Chromatin interaction
ENSG00000240889	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1106846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11977567	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17622717	1.00[YRI][hapmap]
rs17695341	1.00[YRI][hapmap]
rs17695623	1.00[YRI][hapmap]
rs17695707	1.00[YRI][hapmap]
rs28828674	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2907951	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2907952	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2908235	0.96[EUR][1000 genomes]
rs2930315	0.82[CEU][hapmap]
rs2930316	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2930317	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2930323	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2930325	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]
rs2930326	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2930328	1.00[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap]
rs2930329	1.00[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap]
rs2930330	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2930332	0.94[EUR][1000 genomes]
rs2968546	0.85[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2968554	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2968556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6969644	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6977496	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7785630	0.82[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7802537	1.00[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][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	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2930320	ADCK2	cis	Nerve Tibial	GTEx
rs2930320	ADCK2	Cis_1M	lymphoblastoid	RTeQTL
rs2930320	ADCK2	cis	parietal	SCAN
rs2930320	TRIM24	cis	parietal	SCAN
rs2930320	MYBPC2	trans	lymphoblastoid	seeQTL
rs2930320	MRPS33	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140372600-140375800	Enhancers	Fetal Brain Male	brain
2	chr7:140373400-140383200	Weak transcription	HSMMtube	muscle
3	chr7:140373600-140377800	Enhancers	Primary B cells from cord blood	blood
4	chr7:140373600-140385400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr7:140373800-140375800	Weak transcription	Ovary	ovary
6	chr7:140373800-140376000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr7:140373800-140376800	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr7:140373800-140378200	Enhancers	Primary B cells from peripheral blood	blood
9	chr7:140373800-140378800	Weak transcription	Left Ventricle	heart
10	chr7:140373800-140380200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr7:140373800-140395600	Weak transcription	NH-A	brain
12	chr7:140373800-140395800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr7:140373800-140396000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr7:140374000-140375800	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr7:140374000-140376000	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr7:140374000-140376000	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr7:140374000-140376200	Enhancers	Adipose Nuclei	Adipose
18	chr7:140374000-140377400	Weak transcription	Gastric	stomach
19	chr7:140374000-140377800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr7:140374000-140379000	Weak transcription	Fetal Intestine Large	intestine
21	chr7:140374000-140395800	Weak transcription	Fetal Lung	lung
22	chr7:140374000-140395800	Weak transcription	Right Atrium	heart
23	chr7:140374200-140375800	Enhancers	Primary T cells fromperipheralblood	blood
24	chr7:140374200-140375800	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr7:140374200-140375800	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr7:140374200-140375800	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr7:140374200-140376000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr7:140374200-140376000	Enhancers	Colon Smooth Muscle	Colon
29	chr7:140374200-140376200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr7:140374200-140377400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr7:140374200-140377800	Weak transcription	Pancreas	Pancrea
32	chr7:140374200-140395800	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr7:140374200-140396000	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr7:140374200-140396000	Weak transcription	Psoas Muscle	Psoas
35	chr7:140374400-140376400	Enhancers	Brain Substantia Nigra	brain
36	chr7:140374400-140376600	Enhancers	Duodenum Mucosa	Duodenum
37	chr7:140374400-140376800	Weak transcription	Fetal Intestine Small	intestine
38	chr7:140374400-140377600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr7:140374400-140377800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr7:140374400-140378600	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr7:140374400-140395600	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr7:140374400-140396200	Weak transcription	Small Intestine	intestine
43	chr7:140374600-140375800	Enhancers	Brain Angular Gyrus	brain
44	chr7:140374600-140375800	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr7:140374600-140375800	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr7:140374600-140376000	Enhancers	Brain Cingulate Gyrus	brain
47	chr7:140374600-140377600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr7:140374600-140377600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr7:140374600-140377600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr7:140374600-140377600	Weak transcription	Esophagus	oesophagus

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