Variant report

Variant	rs60697181
Chromosome Location	chr7:99642881-99642882
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:99641779..99643919-chr7:99645820..99648790,3	MCF-7	breast:
2	chr7:99641072..99643991-chr7:99644597..99648026,3	K562	blood:
3	chr7:99609453..99615014-chr7:99637646..99644800,9	K562	blood:
4	chr7:99641904..99644254-chr7:99645543..99647997,5	MCF-7	breast:
5	chr7:99641713..99644044-chr7:99645502..99647658,2	K562	blood:
6	chr7:99641810..99643993-chr7:99649500..99651035,2	MCF-7	breast:
7	chr7:99591473..99592533-chr7:99642040..99642986,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000106261	Chromatin interaction
ENSG00000166529	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11558475	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11558476	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12531809	0.82[ASN][1000 genomes]
rs12532238	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12673441	0.82[ASN][1000 genomes]
rs13238380	0.82[ASN][1000 genomes]
rs2897075	0.82[ASN][1000 genomes]
rs35228488	0.82[ASN][1000 genomes]
rs4308665	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4421299	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4727445	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4729573	0.81[ASN][1000 genomes]
rs55969052	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56054049	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6592	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67091024	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67110214	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs68038211	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6963345	0.82[ASN][1000 genomes]
rs72615158	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72615159	0.82[ASN][1000 genomes]
rs73158411	0.81[ASN][1000 genomes]
rs7780686	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7796006	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7803317	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs941289	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
4	nsv469687	chr7:99572543-99755141	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
5	nsv482601	chr7:99572543-99755141	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers 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 miRNA target site	1115 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs60697181	LOC389541	Cis_1M	lymphoblastoid	RTeQTL
rs60697181	TRIM4	Cis_1M	lymphoblastoid	RTeQTL
rs60697181	PVRIG	Cis_1M	lymphoblastoid	RTeQTL
rs60697181	PILRB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99631800-99647000	Weak transcription	Colonic Mucosa	Colon
2	chr7:99632600-99646600	Weak transcription	Fetal Heart	heart
3	chr7:99633000-99646600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr7:99633600-99646400	Weak transcription	Pancreas	Pancrea
5	chr7:99633600-99646600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr7:99633600-99646600	Weak transcription	Colon Smooth Muscle	Colon
7	chr7:99633600-99646600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr7:99633600-99646600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr7:99633600-99646800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr7:99633600-99646800	Weak transcription	Psoas Muscle	Psoas
11	chr7:99633600-99647000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr7:99633800-99646400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr7:99633800-99646400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr7:99633800-99646600	Weak transcription	Esophagus	oesophagus
15	chr7:99633800-99646600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr7:99633800-99647000	Weak transcription	Gastric	stomach
17	chr7:99634000-99646600	Weak transcription	HMEC	breast
18	chr7:99634000-99647000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr7:99634000-99647000	Weak transcription	Left Ventricle	heart
20	chr7:99634000-99647000	Weak transcription	NHLF	lung
21	chr7:99634200-99646600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr7:99634200-99647000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:99635000-99646600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr7:99635000-99646600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr7:99635000-99646800	Weak transcription	HSMMtube	muscle
26	chr7:99635200-99646800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr7:99635200-99646800	Weak transcription	Hela-S3	cervix
28	chr7:99635200-99646800	Weak transcription	NHDF-Ad	bronchial
29	chr7:99635200-99647000	Weak transcription	Ovary	ovary
30	chr7:99635400-99646000	Weak transcription	Stomach Mucosa	stomach
31	chr7:99635400-99646800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr7:99635600-99646400	Weak transcription	Fetal Intestine Small	intestine
33	chr7:99635600-99646800	Weak transcription	Thymus	Thymus
34	chr7:99635800-99646600	Weak transcription	Fetal Intestine Large	intestine
35	chr7:99636000-99646800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr7:99636000-99646800	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr7:99636200-99646400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr7:99636200-99646400	Weak transcription	HSMM	muscle
39	chr7:99636200-99646600	Weak transcription	Fetal Kidney	kidney
40	chr7:99636200-99646800	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr7:99636200-99646800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr7:99636200-99646800	Weak transcription	Fetal Brain Female	brain
43	chr7:99636200-99646800	Weak transcription	NH-A	brain
44	chr7:99636200-99647000	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr7:99636200-99647000	Weak transcription	Fetal Muscle Leg	muscle
46	chr7:99636400-99646600	Weak transcription	Dnd41	blood
47	chr7:99636400-99646800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr7:99636400-99646800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr7:99636400-99646800	Weak transcription	Stomach Smooth Muscle	stomach
50	chr7:99636400-99647000	Weak transcription	Fetal Muscle Trunk	muscle

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