Variant report

Variant	rs6950688
Chromosome Location	chr7:65339517-65339518
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	chr7:65214366..65217502-chr7:65337041..65339664,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228409	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1084094	0.83[EUR][1000 genomes]
rs10950014	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10950015	0.93[EUR][1000 genomes]
rs10950018	0.91[EUR][1000 genomes]
rs10950021	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10950022	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1167398	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11767030	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11773552	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12532875	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12532877	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12534626	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12535204	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12538430	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12540589	0.86[EUR][1000 genomes]
rs12671816	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2420048	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs313811	0.82[EUR][1000 genomes]
rs401176	0.81[EUR][1000 genomes]
rs4535605	0.93[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs453835	0.81[EUR][1000 genomes]
rs4717280	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4718287	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4718296	0.87[EUR][1000 genomes]
rs59187325	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60711791	0.82[EUR][1000 genomes]
rs6460265	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6460266	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6950821	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6958860	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6959267	0.86[EUR][1000 genomes]
rs6971490	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6971690	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73142138	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73142150	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73142153	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73142155	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73148071	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7786356	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7800210	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7803283	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7807457	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429767	chr7:64473713-65415647	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	esv3339156	chr7:64510176-65349050	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv2759534	chr7:64551274-65373851	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv427788	chr7:64551274-65390424	Weak transcription Active TSS Strong transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	esv2764020	chr7:64594065-65351820	Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv1029942	chr7:64679680-65371565	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv538903	chr7:64679680-65371565	Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
8	nsv1019667	chr7:64679680-65380603	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
9	esv2757227	chr7:64694241-65373851	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
10	nsv1025207	chr7:65092426-65339879	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
11	nsv1033400	chr7:65092426-65339879	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
12	esv2761079	chr7:65092426-65689733	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
13	nsv1020622	chr7:65161364-65339879	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
14	nsv1029800	chr7:65309327-65367692	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	esv3427026	chr7:65336942-65339890	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
16	esv3414148	chr7:65337017-65339740	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6950688	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs6950688	RP11-479O9.2	cis	lung	GTEx
rs6950688	RP4-756H11.3	cis	Thyroid	GTEx
rs6950688	INTS4L1	cis	Muscle Skeletal	GTEx
rs6950688	INTS4L1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65337400-65339600	Active TSS	A549	lung
2	chr7:65337600-65339600	Active TSS	H9 Cell Line	embryonic stem cell
3	chr7:65337600-65339600	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr7:65337600-65339600	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr7:65337600-65339600	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr7:65337600-65339600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr7:65337600-65339600	Active TSS	Brain Angular Gyrus	brain
8	chr7:65337600-65339600	Active TSS	Brain Anterior Caudate	brain
9	chr7:65337600-65339600	Active TSS	Brain Cingulate Gyrus	brain
10	chr7:65337600-65339600	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr7:65337600-65339600	Active TSS	HMEC	breast
12	chr7:65337600-65340000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
13	chr7:65337600-65340000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr7:65337800-65339600	Active TSS	Brain Germinal Matrix	brain
15	chr7:65338000-65339600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr7:65338200-65339600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr7:65338200-65339600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr7:65338200-65339600	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr7:65338200-65339600	Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr7:65338200-65339600	Active TSS	Muscle Satellite Cultured Cells	--
21	chr7:65338200-65339600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr7:65338200-65339600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr7:65338200-65339600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr7:65338200-65339600	Active TSS	Colonic Mucosa	Colon
25	chr7:65338200-65339600	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr7:65338200-65339600	Active TSS	Fetal Stomach	stomach
27	chr7:65338200-65339600	Active TSS	Right Ventricle	heart
28	chr7:65338200-65339600	Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr7:65338200-65339600	Active TSS	NHLF	lung
30	chr7:65338400-65339600	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr7:65338400-65339600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr7:65338400-65339600	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr7:65338400-65339600	Active TSS	Rectal Mucosa Donor 29	rectum
34	chr7:65338400-65339600	Active TSS	NHEK	skin
35	chr7:65338400-65340000	Active TSS	GM12878-XiMat	blood
36	chr7:65338400-65341200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr7:65338800-65339600	Active TSS	Stomach Mucosa	stomach
38	chr7:65339000-65339600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr7:65339000-65339600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr7:65339000-65339600	Flanking Active TSS	Fetal Brain Female	brain
41	chr7:65339000-65339600	Flanking Active TSS	Fetal Muscle Leg	muscle
42	chr7:65339000-65339600	Bivalent/Poised TSS	HepG2	liver
43	chr7:65339000-65339600	Flanking Active TSS	HUVEC	blood vessel
44	chr7:65339000-65339600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr7:65339200-65339600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr7:65339200-65339600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr7:65339200-65339600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr7:65339200-65339600	Flanking Active TSS	Duodenum Mucosa	Duodenum
49	chr7:65339200-65339600	Flanking Active TSS	Fetal Lung	lung
50	chr7:65339200-65339600	Enhancers	Gastric	stomach

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