Variant report

Variant	rs322790
Chromosome Location	chr7:127749000-127749001
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:127623989..127624531-chr7:127748891..127749488,2	MCF-7	breast:
2	chr7:127747173..127749516-chr7:127758374..127760292,2	K562	blood:
3	chr7:127746979..127749085-chr7:127751994..127753543,2	K562	blood:
4	chr7:127748855..127752191-chr7:127753186..127755504,3	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs178733	0.81[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs184430	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs322738	0.84[ASN][1000 genomes]
rs322752	0.81[ASN][1000 genomes]
rs322755	0.81[EUR][1000 genomes]
rs322756	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs322760	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs322761	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs322762	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs322765	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs322766	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs322768	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs322770	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs322771	0.89[ASN][1000 genomes]
rs322775	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs322778	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs322780	0.95[ASN][1000 genomes]
rs322782	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs322783	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs322784	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs322785	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs322786	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs322787	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs322791	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs322806	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs322807	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs322808	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs322809	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs322811	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs322812	0.81[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs322815	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs322818	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.83[LWK][hapmap];0.86[YRI][hapmap];0.97[ASN][1000 genomes]
rs5028619	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6467162	0.81[AFR][1000 genomes]
rs6960004	0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[ASN][1000 genomes]
rs7811971	0.84[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs322790	EEF2K	trans	cerebellum	SCAN
rs322790	CCDC136	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127744600-127761600	Weak transcription	Right Atrium	heart
2	chr7:127744800-127753200	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr7:127744800-127753400	Enhancers	Primary B cells from peripheral blood	blood
4	chr7:127745800-127749000	Enhancers	Primary T cells fromperipheralblood	blood
5	chr7:127746400-127753400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr7:127746800-127749000	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr7:127746800-127749000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr7:127747000-127749200	Enhancers	Fetal Thymus	thymus
9	chr7:127747000-127753400	Enhancers	Thymus	Thymus
10	chr7:127747200-127749600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
11	chr7:127747400-127750000	Enhancers	Primary hematopoietic stem cells	blood
12	chr7:127747600-127749000	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr7:127747800-127749400	Enhancers	Spleen	Spleen
14	chr7:127747800-127753000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr7:127748200-127749200	Enhancers	Dnd41	blood
16	chr7:127748200-127749800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr7:127748200-127750200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr7:127748200-127751400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr7:127748200-127751400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr7:127748400-127749000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr7:127748400-127749000	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr7:127748400-127749200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr7:127748400-127749200	Enhancers	Fetal Brain Female	brain
24	chr7:127748400-127749400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr7:127748400-127749400	Enhancers	Brain Anterior Caudate	brain
26	chr7:127748400-127749600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr7:127748400-127749800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr7:127748400-127749800	Flanking Active TSS	Primary T cells from cord blood	blood
29	chr7:127748400-127749800	Enhancers	Placenta	Placenta
30	chr7:127748400-127749800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr7:127748400-127750000	Flanking Active TSS	GM12878-XiMat	blood
32	chr7:127748600-127749400	Bivalent Enhancer	Adipose Nuclei	Adipose
33	chr7:127748600-127749400	Enhancers	Brain Angular Gyrus	brain
34	chr7:127748600-127749400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
35	chr7:127748600-127749600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
36	chr7:127748600-127749600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
37	chr7:127748600-127749600	Enhancers	Fetal Brain Male	brain
38	chr7:127748600-127749800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr7:127748600-127749800	Bivalent Enhancer	Fetal Intestine Small	intestine
40	chr7:127748800-127749000	Enhancers	Brain Cingulate Gyrus	brain
41	chr7:127748800-127749000	Bivalent Enhancer	Fetal Muscle Leg	muscle
42	chr7:127748800-127749000	Bivalent Enhancer	Stomach Mucosa	stomach
43	chr7:127748800-127749000	Bivalent Enhancer	NHEK	skin
44	chr7:127748800-127749400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr7:127748800-127749400	Enhancers	Duodenum Mucosa	Duodenum
46	chr7:127748800-127749600	Flanking Active TSS	Primary B cells from cord blood	blood
47	chr7:127748800-127749800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr7:127748800-127751200	Weak transcription	Brain Substantia Nigra	brain
49	chr7:127749000-127749200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
50	chr7:127749000-127749200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

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