Variant report

Variant	rs6970119
Chromosome Location	chr7:140091884-140091885
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:140091825..140093719-chr7:140095231..140098227,2	MCF-7	breast:
2	chr7:140090494..140093005-chr7:140100904..140104008,3	K562	blood:
3	chr7:140089947..140093642-chr7:140094794..140098474,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157800	Chromatin interaction
ENSG00000146955	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10251020	0.85[EUR][1000 genomes]
rs10261444	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12703828	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13229539	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13235719	0.81[EUR][1000 genomes]
rs13236204	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13246775	0.81[EUR][1000 genomes]
rs62490400	0.81[EUR][1000 genomes]
rs6978505	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9640466	0.81[CEU][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022919	chr7:140043299-140120546	Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2762706	chr7:140054170-140119629	Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv522190	chr7:140066411-140130663	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6970119	OR9A2	cis	cerebellum	SCAN
rs6970119	MGAM	cis	parietal	SCAN
rs6970119	ZC3HAV1L	cis	parietal	SCAN
rs6970119	CREB3L2	cis	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140033600-140096000	Weak transcription	Stomach Mucosa	stomach
2	chr7:140052000-140097400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:140058600-140096000	Weak transcription	Small Intestine	intestine
4	chr7:140058800-140097200	Weak transcription	Brain Anterior Caudate	brain
5	chr7:140076800-140096200	Weak transcription	NHLF	lung
6	chr7:140080200-140095800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr7:140080200-140096000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr7:140080200-140097200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr7:140080200-140097200	Weak transcription	HSMMtube	muscle
10	chr7:140080200-140097600	Weak transcription	Brain Angular Gyrus	brain
11	chr7:140080600-140096200	Weak transcription	HepG2	liver
12	chr7:140080600-140097400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr7:140080800-140096200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr7:140081400-140097200	Weak transcription	Brain Germinal Matrix	brain
15	chr7:140081800-140093000	Weak transcription	Fetal Intestine Small	intestine
16	chr7:140082200-140093000	Weak transcription	Fetal Stomach	stomach
17	chr7:140082200-140096200	Weak transcription	Fetal Lung	lung
18	chr7:140082200-140097000	Weak transcription	Fetal Brain Female	brain
19	chr7:140082200-140097400	Weak transcription	Right Ventricle	heart
20	chr7:140082400-140092800	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr7:140082400-140093000	Weak transcription	Lung	lung
22	chr7:140082400-140093200	Weak transcription	Left Ventricle	heart
23	chr7:140082400-140095800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr7:140082400-140096000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr7:140082400-140096000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr7:140082400-140096400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr7:140082400-140096600	Weak transcription	Fetal Muscle Trunk	muscle
28	chr7:140082400-140096600	Weak transcription	Fetal Muscle Leg	muscle
29	chr7:140082400-140097000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr7:140082400-140097200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr7:140082400-140097200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr7:140082400-140097400	Weak transcription	Fetal Intestine Large	intestine
33	chr7:140082400-140097400	Weak transcription	Ovary	ovary
34	chr7:140084600-140096000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr7:140084800-140093000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr7:140085000-140093000	Weak transcription	NHEK	skin
37	chr7:140086200-140097200	Weak transcription	Psoas Muscle	Psoas
38	chr7:140086600-140092000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr7:140086600-140096000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr7:140086800-140092800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr7:140086800-140097200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr7:140087600-140093400	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr7:140088800-140092000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr7:140088800-140092600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
45	chr7:140089000-140092000	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr7:140089000-140092000	Enhancers	Primary B cells from peripheral blood	blood
47	chr7:140089000-140092200	Enhancers	Primary T cells fromperipheralblood	blood
48	chr7:140089200-140092200	Enhancers	H9 Cell Line	embryonic stem cell
49	chr7:140089200-140092200	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr7:140089400-140092000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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