Variant report

Variant	rs6947388
Chromosome Location	chr7:104639583-104639584
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:104637895..104640816-chr7:105263916..105266780,2	K562	blood:
2	chr7:104580498..104582550-chr7:104638156..104639691,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SRPK2-1	chr7:104637584-104654636	NONHSAT122594

Variant related genes	Relation type
ENSG00000146776	Chromatin interaction
ENSG00000237513	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1011468	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10228174	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10247691	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10252714	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10263499	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1029596	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11978288	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11981882	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12534212	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12705296	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2097942	0.87[EUR][1000 genomes]
rs2106500	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2299298	0.86[EUR][1000 genomes]
rs4602821	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4727618	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730066	0.93[ASN][1000 genomes]
rs56016333	0.86[ASN][1000 genomes]
rs6466035	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67665940	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6950894	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6963395	0.88[EUR][1000 genomes]
rs6976394	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6980244	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784126	0.86[EUR][1000 genomes]
rs888086	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9918494	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029283	chr7:104571741-104729168	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	132 gene(s)	inside rSNPs	diseases
2	nsv888927	chr7:104614664-104781644	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
3	esv2829879	chr7:104618318-104652671	Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv608068	chr7:104622402-104757483	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv437561	chr7:104626690-104647571	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv437995	chr7:104632980-104641241	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1022083	chr7:104634376-104644391	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:104625000-104641200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:104625000-104647400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:104625200-104643800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr7:104625400-104643000	Weak transcription	Fetal Brain Female	brain
5	chr7:104625800-104641200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr7:104626200-104641600	Weak transcription	Brain Germinal Matrix	brain
7	chr7:104626400-104639600	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr7:104627000-104641000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr7:104627400-104643600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:104629800-104640200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr7:104629800-104641200	Weak transcription	Colonic Mucosa	Colon
12	chr7:104630200-104641200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr7:104630800-104640200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr7:104630800-104641600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr7:104630800-104643600	Weak transcription	Fetal Kidney	kidney
16	chr7:104631600-104643600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr7:104632000-104641200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr7:104632200-104640600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr7:104632200-104641200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr7:104632200-104641200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr7:104632200-104641200	Weak transcription	Esophagus	oesophagus
22	chr7:104632200-104641200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr7:104632200-104641200	Weak transcription	Fetal Muscle Leg	muscle
24	chr7:104632200-104641200	Weak transcription	Gastric	stomach
25	chr7:104632200-104641200	Weak transcription	Pancreas	Pancrea
26	chr7:104632200-104641200	Weak transcription	Spleen	Spleen
27	chr7:104632800-104641200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr7:104632800-104641200	Weak transcription	Fetal Stomach	stomach
29	chr7:104632800-104641400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr7:104633000-104642600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr7:104633200-104643600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr7:104633400-104641400	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr7:104633600-104650400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr7:104634000-104647200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr7:104634200-104640200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr7:104634400-104641200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr7:104634400-104642800	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr7:104634400-104642800	Weak transcription	HSMMtube	muscle
39	chr7:104634600-104639600	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr7:104634600-104640200	Strong transcription	HSMM	muscle
41	chr7:104634600-104640800	Weak transcription	Right Ventricle	heart
42	chr7:104634800-104641800	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr7:104635000-104640600	Weak transcription	NHLF	lung
44	chr7:104635200-104642800	Weak transcription	NH-A	brain
45	chr7:104635400-104640200	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr7:104635400-104641400	Enhancers	Primary T cells from cord blood	blood
47	chr7:104635400-104641400	Weak transcription	Aorta	Aorta
48	chr7:104635400-104641800	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr7:104635400-104642200	Weak transcription	Brain Substantia Nigra	brain
50	chr7:104635400-104643200	Weak transcription	HUVEC	blood vessel

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