Variant report

Variant	rs6965144
Chromosome Location	chr7:117822559-117822560
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	POLR2A	chr7:117820845-117829160	K562	blood:	n/a	n/a
2	POLR2A	chr7:117822373-117822832	HepG2	liver:	n/a	n/a
3	POLR2A	chr7:117822340-117822884	GM12878	blood:	n/a	n/a
4	POLR2A	chr7:117822010-117826055	GM12891	blood:	n/a	n/a
5	POLR2A	chr7:117822283-117822853	K562	blood:	n/a	n/a
6	POLR2A	chr7:117822224-117822873	GM12878	blood:	n/a	n/a
7	IRF1	chr7:117822511-117825605	K562	blood:	n/a	chr7:117823522-117823535 chr7:117825228-117825244 chr7:117822936-117822950 chr7:117824214-117824228 chr7:117824218-117824232 chr7:117824218-117824228
8	POLR2A	chr7:117822512-117825871	GM12878	blood:	n/a	n/a
9	POLR2A	chr7:117822305-117822568	MCF-7	breast:	n/a	n/a
10	CTCF	chr7:117822512-117822618	GM13976	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:117388690..117390929-chr7:117821238..117823244,2	MCF-7	breast:
2	chr5:149864249..149866469-chr7:117821128..117824020,2	MCF-7	breast:
3	chr7:117821578..117823325-chr7:117847731..117849389,2	K562	blood:
4	chr7:117819950..117822921-chr7:117839591..117842038,2	MCF-7	breast:
5	chr7:117822159..117825807-chr7:117854196..117858736,4	K562	blood:
6	chr7:117821797..117823895-chr7:117873522..117875796,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTTNBP2-3	chr7:117821706-117824013	NONHSAT122959

Variant related genes	Relation type
NAA38	TF binding region
ENSG00000070614	Chromatin interaction
ENSG00000106013	Chromatin interaction
ENSG00000254333	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10085904	0.93[EUR][1000 genomes]
rs10226152	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10227326	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10229589	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10241875	0.89[EUR][1000 genomes]
rs10252627	0.88[EUR][1000 genomes]
rs10267938	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10487390	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1054032	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1061731	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10953864	0.94[EUR][1000 genomes]
rs1117254	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11486992	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11543742	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11770353	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11979012	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12112697	0.82[EUR][1000 genomes]
rs12537795	0.94[EUR][1000 genomes]
rs12667103	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12673046	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13224733	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2041527	0.81[EUR][1000 genomes]
rs2041528	0.81[EUR][1000 genomes]
rs2058416	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2058417	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2191920	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2402322	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2896242	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3802012	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4141028	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41900	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41901	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41902	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41905	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41906	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41909	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41910	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs41911	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs41915	0.90[EUR][1000 genomes]
rs41916	0.90[EUR][1000 genomes]
rs41926	0.90[EUR][1000 genomes]
rs41933	0.88[EUR][1000 genomes]
rs41934	0.90[EUR][1000 genomes]
rs41935	0.90[EUR][1000 genomes]
rs41938	0.90[EUR][1000 genomes]
rs41939	0.90[EUR][1000 genomes]
rs41945	0.80[EUR][1000 genomes]
rs41960	0.84[EUR][1000 genomes]
rs5002233	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6466650	0.84[EUR][1000 genomes]
rs6944524	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6946855	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6948096	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6956486	0.94[EUR][1000 genomes]
rs6964911	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7779933	0.93[EUR][1000 genomes]
rs7796145	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7796148	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7797855	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7799229	0.92[EUR][1000 genomes]
rs7806490	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs917761	0.91[EUR][1000 genomes]
rs9655829	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9656260	0.94[EUR][1000 genomes]
rs979652	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9886333	0.82[EUR][1000 genomes]
rs989899	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869971	chr7:117420583-118274149	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv889088	chr7:117744660-117913648	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:117816000-117822600	Weak transcription	NHEK	skin
2	chr7:117816200-117822800	Weak transcription	Fetal Heart	heart
3	chr7:117816400-117822800	Weak transcription	Primary B cells from cord blood	blood
4	chr7:117818800-117822800	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr7:117819200-117822800	Weak transcription	K562	blood
6	chr7:117820600-117822800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr7:117820800-117823400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr7:117821600-117822600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr7:117822000-117822600	Enhancers	Fetal Kidney	kidney
10	chr7:117822200-117822800	Enhancers	Dnd41	blood
11	chr7:117822400-117822600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr7:117822400-117822600	Flanking Active TSS	Fetal Intestine Small	intestine
13	chr7:117822400-117822600	Enhancers	Lung	lung
14	chr7:117822400-117822600	Enhancers	Stomach Mucosa	stomach
15	chr7:117822400-117823000	Active TSS	Liver	Liver
16	chr7:117822400-117823000	Active TSS	Duodenum Mucosa	Duodenum
17	chr7:117822400-117823000	Enhancers	Pancreas	Pancrea
18	chr7:117822400-117823200	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr7:117822400-117823200	Enhancers	Primary B cells from peripheral blood	blood
20	chr7:117822400-117823200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr7:117822400-117823200	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr7:117822400-117824800	Active TSS	Gastric	stomach
23	chr7:117822400-117825000	Active TSS	Fetal Intestine Large	intestine
24	chr7:117822400-117825600	Active TSS	Pancreatic Islets	Pancreatic Islet

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