Variant report

Variant	rs9470716
Chromosome Location	chr6:37805239-37805240
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:37803626..37806524-chr6:37806785..37809778,2	K562	blood:
2	chr6:37785728..37788971-chr6:37803149..37806338,4	K562	blood:
3	chr6:37802735..37804410-chr6:37804516..37806911,2	MCF-7	breast:
4	chr6:37787471..37790719-chr6:37803149..37805548,4	K562	blood:
5	chr6:37793853..37796744-chr6:37803996..37806760,2	K562	blood:

Variant related genes	Relation type
ENSG00000156639	Chromatin interaction
ENSG00000225945	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10046397	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10080245	1.00[EUR][1000 genomes]
rs11966394	1.00[MEX][hapmap]
rs12178911	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2842518	1.00[TSI][hapmap]
rs56958593	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57527781	0.96[AFR][1000 genomes]
rs58305294	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58698408	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58860274	1.00[EUR][1000 genomes]
rs60997161	1.00[EUR][1000 genomes]
rs6904932	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs6906120	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6912045	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6924117	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6926669	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6930823	0.90[AMR][1000 genomes]
rs73730817	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73730818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73730823	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73730827	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73730832	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73730849	1.00[EUR][1000 genomes]
rs7756841	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7765448	1.00[EUR][1000 genomes]
rs7769848	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9462350	1.00[MEX][hapmap]
rs9462362	1.00[EUR][1000 genomes]
rs9462367	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9462370	1.00[EUR][1000 genomes]
rs9462371	1.00[EUR][1000 genomes]
rs9462375	1.00[EUR][1000 genomes]
rs9470657	1.00[MEX][hapmap]
rs9470659	1.00[MEX][hapmap]
rs9470707	1.00[TSI][hapmap];0.90[AMR][1000 genomes]
rs9470711	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9470715	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9470717	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9470719	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9470722	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9470729	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9470731	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9470733	1.00[EUR][1000 genomes]
rs9470736	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9470744	1.00[ASW][hapmap];0.96[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs9470745	1.00[EUR][1000 genomes]

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	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1017051	chr6:37789341-38084719	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv538203	chr6:37789341-38084719	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9470716	CD3D	trans	lymphoblastoid	seeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37791200-37820000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:37791400-37810200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:37791400-37813400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr6:37791400-37816000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr6:37793800-37813600	Weak transcription	NH-A	brain
6	chr6:37794000-37819800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:37795000-37813800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr6:37795000-37825600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr6:37795800-37813400	Weak transcription	HSMMtube	muscle
10	chr6:37796000-37812800	Weak transcription	Colonic Mucosa	Colon
11	chr6:37796000-37813200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr6:37796000-37813800	Weak transcription	NHDF-Ad	bronchial
13	chr6:37796000-37815600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr6:37796000-37828800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr6:37796000-37830600	Weak transcription	Hela-S3	cervix
16	chr6:37796200-37811400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr6:37796200-37813200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr6:37797800-37808200	Weak transcription	Brain Anterior Caudate	brain
19	chr6:37798400-37805600	Weak transcription	Osteobl	bone
20	chr6:37798400-37812800	Weak transcription	HSMM	muscle
21	chr6:37798400-37815200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr6:37798400-37815800	Weak transcription	Fetal Heart	heart
23	chr6:37799000-37808400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:37799400-37817400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr6:37799600-37806600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr6:37799600-37808000	Weak transcription	K562	blood
27	chr6:37799600-37809400	Weak transcription	Lung	lung
28	chr6:37799600-37811200	Weak transcription	Brain Substantia Nigra	brain
29	chr6:37799600-37811800	Weak transcription	Placenta	Placenta
30	chr6:37799600-37812800	Weak transcription	NHEK	skin
31	chr6:37799600-37813400	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr6:37799600-37825800	Weak transcription	Esophagus	oesophagus
33	chr6:37799800-37805800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:37799800-37825400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr6:37800000-37808200	Weak transcription	Liver	Liver
36	chr6:37800200-37812800	Weak transcription	Gastric	stomach
37	chr6:37800200-37813400	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr6:37800200-37830200	Weak transcription	Ovary	ovary
39	chr6:37800200-37836200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr6:37800400-37807800	Weak transcription	HepG2	liver
41	chr6:37800400-37813200	Weak transcription	Colon Smooth Muscle	Colon
42	chr6:37800600-37809600	Weak transcription	Small Intestine	intestine
43	chr6:37800800-37809600	Weak transcription	Right Ventricle	heart
44	chr6:37801000-37805400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr6:37801000-37805600	Weak transcription	Right Atrium	heart
46	chr6:37801000-37807400	Weak transcription	Psoas Muscle	Psoas
47	chr6:37801000-37809400	Weak transcription	Left Ventricle	heart
48	chr6:37801000-37811400	Weak transcription	Thymus	Thymus
49	chr6:37801000-37811600	Weak transcription	Fetal Thymus	thymus
50	chr6:37801000-37811800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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