Variant report

Variant	rs6973092
Chromosome Location	chr7:127660620-127660621
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:127660077..127660876-chr7:127848654..127849189,2	K562	blood:
2	chr7:127660248..127660952-chr7:127718023..127718768,2	MCF-7	breast:
3	chr7:127651652..127655831-chr7:127659275..127661755,4	K562	blood:
4	chr7:127651063..127656520-chr7:127658090..127661426,7	K562	blood:
5	chr7:127660092..127663407-chr7:127669055..127671780,3	MCF-7	breast:
6	chr7:127659087..127661420-chr7:127663957..127667056,3	K562	blood:
7	chr7:127660337..127660859-chr7:127849677..127850423,2	K562	blood:
8	chr7:127658157..127661100-chr7:127671141..127673434,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000128594	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1193336	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs124756	0.83[JPT][hapmap]
rs12668077	0.87[JPT][hapmap]
rs1345509	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1419968	0.96[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.88[EUR][1000 genomes]
rs17732677	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs178734	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2241291	0.94[JPT][hapmap]
rs225241	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs322813	0.83[JPT][hapmap]
rs322819	0.83[JPT][hapmap]
rs322820	0.83[JPT][hapmap]
rs322821	0.83[JPT][hapmap]
rs322823	0.83[JPT][hapmap]
rs322826	0.84[GIH][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs322827	0.85[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];0.81[ASN][1000 genomes]
rs322828	0.85[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];0.81[ASN][1000 genomes]
rs322831	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs322832	0.82[EUR][1000 genomes]
rs322833	0.82[EUR][1000 genomes]
rs322834	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs322835	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs322836	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs322838	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs322840	0.83[JPT][hapmap]
rs35774036	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3757753	0.82[EUR][1000 genomes]
rs3757755	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3757760	0.94[JPT][hapmap]
rs3757763	0.94[JPT][hapmap]
rs3779523	0.83[JPT][hapmap]
rs3779526	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3808056	0.85[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs3808061	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3808077	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3808082	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3808088	0.87[JPT][hapmap]
rs3823995	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4731386	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6944446	0.83[CHB][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv1016143	chr7:127251359-127726762	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1024743	chr7:127498695-127670004	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6973092	TMEM209	cis	cerebellum	SCAN
rs6973092	ARF5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127631800-127660800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr7:127636000-127662400	Weak transcription	NHDF-Ad	bronchial
3	chr7:127641600-127670400	Weak transcription	Colonic Mucosa	Colon
4	chr7:127644000-127668800	Weak transcription	Dnd41	blood
5	chr7:127644000-127670200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr7:127644800-127667400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr7:127644800-127670800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr7:127645000-127684000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr7:127645200-127661800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr7:127645400-127670000	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr7:127651800-127661600	Strong transcription	Fetal Intestine Small	intestine
12	chr7:127651800-127664400	Weak transcription	Right Ventricle	heart
13	chr7:127651800-127665600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr7:127651800-127667600	Weak transcription	Colon Smooth Muscle	Colon
15	chr7:127651800-127668800	Weak transcription	Ovary	ovary
16	chr7:127651800-127670600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr7:127653000-127661000	Weak transcription	A549	lung
18	chr7:127653200-127668800	Weak transcription	Thymus	Thymus
19	chr7:127653400-127661200	Weak transcription	NHLF	lung
20	chr7:127653400-127662400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr7:127654600-127669200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr7:127654800-127664200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr7:127656600-127662200	Strong transcription	Duodenum Mucosa	Duodenum
24	chr7:127657000-127661600	Enhancers	Brain Angular Gyrus	brain
25	chr7:127657000-127661600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr7:127657000-127662000	Strong transcription	Primary T cells from cord blood	blood
27	chr7:127657000-127664600	Strong transcription	GM12878-XiMat	blood
28	chr7:127657000-127670200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr7:127657200-127660800	Enhancers	H1 Cell Line	embryonic stem cell
30	chr7:127657200-127661600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr7:127657200-127661600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr7:127657200-127661800	Strong transcription	Primary B cells from peripheral blood	blood
33	chr7:127657200-127663800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr7:127657400-127661000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr7:127657400-127661000	Genic enhancers	Fetal Brain Female	brain
36	chr7:127657600-127661800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr7:127657600-127661800	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr7:127657800-127660800	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr7:127657800-127661600	Enhancers	Brain Cingulate Gyrus	brain
40	chr7:127657800-127663200	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr7:127657800-127669200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr7:127658000-127661000	Genic enhancers	Brain Germinal Matrix	brain
43	chr7:127658000-127668800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr7:127658200-127663000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr7:127658400-127661400	Weak transcription	NH-A	brain
46	chr7:127658400-127661400	Weak transcription	Osteobl	bone
47	chr7:127658400-127666600	Weak transcription	Stomach Smooth Muscle	stomach
48	chr7:127658600-127661400	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr7:127658600-127661400	Weak transcription	HUVEC	blood vessel
50	chr7:127658600-127661800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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