Variant report

Variant	rs6964936
Chromosome Location	chr7:127943131-127943132
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:127942755-127943725	K562	blood:	n/a	n/a
2	POLR2A	chr7:127942741-127943167	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:127940082..127943532-chr7:127944561..127947795,4	K562	blood:
2	chr7:127941056..127943858-chr7:127948197..127950566,3	K562	blood:
3	chr7:127937053..127939817-chr7:127940949..127943521,2	K562	blood:
4	chr7:127941056..127943858-chr7:127948197..127950137,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RBM28-3	chr7:127937738-127947816	NONHSAT123178

No data

Variant related genes	Relation type
ENSG00000242261	TF binding region
ENSG00000242261	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10236380	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10261176	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11976673	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12533121	0.93[JPT][hapmap]
rs2290225	0.93[JPT][hapmap]
rs359651	0.93[JPT][hapmap]
rs359652	0.93[JPT][hapmap]
rs3750036	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3763395	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58238563	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6954653	0.90[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7794771	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7809696	1.00[ASW][hapmap];0.85[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022385	chr7:127246656-127971194	Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv539120	chr7:127246656-127971194	Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1016669	chr7:127927963-127948122	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1017782	chr7:127928249-127946901	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1019036	chr7:127928441-127948122	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1018630	chr7:127928441-127948604	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	esv2764054	chr7:127928453-127948604	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv525319	chr7:127929271-127946173	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6964936	TNPO3	cis	parietal	SCAN
rs6964936	C7orf68	cis	parietal	SCAN
rs6964936	FHL1	trans	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127917000-127945600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:127917200-127943200	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr7:127920200-127945200	Weak transcription	Right Ventricle	heart
4	chr7:127921800-127944400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr7:127922000-127944400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr7:127922200-127943200	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr7:127923800-127943200	Weak transcription	Pancreas	Pancrea
8	chr7:127924200-127943800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr7:127924600-127950000	Weak transcription	Psoas Muscle	Psoas
10	chr7:127926400-127943200	Weak transcription	HSMM	muscle
11	chr7:127927000-127943200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr7:127927000-127944400	Weak transcription	Ovary	ovary
13	chr7:127928800-127944400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr7:127930800-127949200	Weak transcription	Fetal Kidney	kidney
15	chr7:127931800-127943200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr7:127935800-127943200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr7:127937400-127944400	Weak transcription	Brain Hippocampus Middle	brain
18	chr7:127938600-127943200	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr7:127938600-127944400	Weak transcription	Placenta	Placenta
20	chr7:127938600-127945800	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr7:127938800-127944000	Weak transcription	Brain Substantia Nigra	brain
22	chr7:127938800-127946000	Weak transcription	Colon Smooth Muscle	Colon
23	chr7:127939200-127943400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr7:127939400-127943200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr7:127939400-127943200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr7:127939400-127943200	Weak transcription	Colonic Mucosa	Colon
27	chr7:127939400-127943200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr7:127939400-127943400	Weak transcription	Gastric	stomach
29	chr7:127939400-127943400	Weak transcription	K562	blood
30	chr7:127939400-127945400	Weak transcription	Esophagus	oesophagus
31	chr7:127939400-127946200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr7:127939400-127962800	Weak transcription	Right Atrium	heart
33	chr7:127939600-127943200	Weak transcription	Fetal Thymus	thymus
34	chr7:127939600-127944200	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr7:127939600-127944400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr7:127939600-127944400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr7:127939600-127982200	Weak transcription	Stomach Mucosa	stomach
38	chr7:127939800-127943400	Weak transcription	Fetal Lung	lung
39	chr7:127940000-127944400	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr7:127940000-127946600	Weak transcription	Fetal Heart	heart
41	chr7:127940000-127980800	Strong transcription	Fetal Muscle Trunk	muscle
42	chr7:127940200-127953000	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr7:127940200-127953800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr7:127940200-127955600	Strong transcription	Fetal Stomach	stomach
45	chr7:127940400-127945400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr7:127940400-127946200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr7:127940400-127955400	Strong transcription	Aorta	Aorta
48	chr7:127940400-127980000	Strong transcription	Stomach Smooth Muscle	stomach
49	chr7:127940600-127943200	Weak transcription	Hela-S3	cervix
50	chr7:127940600-127943400	Weak transcription	Primary B cells from peripheral blood	blood

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