Variant report

Variant	rs7456421
Chromosome Location	chr7:139415775-139415776
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:139415237..139415953-chr7:139701565..139702351,2	K562	blood:
2	chr7:139415427..139415927-chr7:139701788..139702308,2	MCF-7	breast:
3	chr7:139415110..139417997-chr7:139418401..139420501,2	MCF-7	breast:
4	chr7:139414543..139416959-chr7:139476449..139479049,2	MCF-7	breast:
5	chr7:139408971..139413688-chr7:139413768..139417072,5	K562	blood:
6	chr7:139412716..139416126-chr7:139473594..139478833,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000064393	Chromatin interaction
ENSG00000059377	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1011017	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1011018	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1015122	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10215942	0.86[ASN][1000 genomes]
rs10236187	0.83[ASN][1000 genomes]
rs10262775	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10278124	0.81[CEU][hapmap]
rs11769215	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11769961	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11770283	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11972982	0.83[ASN][1000 genomes]
rs11983375	0.83[ASN][1000 genomes]
rs12673068	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12703395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1541480	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1860509	0.86[EUR][1000 genomes]
rs2058265	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2109338	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28656273	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4074826	0.81[CEU][hapmap]
rs4074827	0.81[CEU][hapmap]
rs4132077	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4132078	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4725579	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4726459	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4726525	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56152277	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58543521	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6464214	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6464220	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66985026	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6978085	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7459106	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7782128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7790519	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7807797	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7810028	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]

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	nsv1020234	chr7:139377822-139661964	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1032711	chr7:139411404-139684043	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7456421	LOC389562	cis	multi-tissue	Pritchard
rs7456421		cis	Lymphoblastoid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:139404400-139417000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:139404600-139417400	Strong transcription	Primary T cells from cord blood	blood
3	chr7:139407600-139420000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr7:139409800-139420000	Weak transcription	Small Intestine	intestine
5	chr7:139410200-139416800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr7:139411600-139416000	Genic enhancers	Left Ventricle	heart
7	chr7:139411600-139416600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr7:139411600-139416600	Strong transcription	HMEC	breast
9	chr7:139411600-139417000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr7:139411600-139417200	Strong transcription	Stomach Smooth Muscle	stomach
11	chr7:139411600-139417400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr7:139411600-139417400	Strong transcription	HSMM	muscle
13	chr7:139411600-139417600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr7:139411800-139416000	Genic enhancers	Right Ventricle	heart
15	chr7:139411800-139416600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
16	chr7:139411800-139416800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr7:139411800-139416800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr7:139411800-139416800	Strong transcription	Fetal Thymus	thymus
19	chr7:139411800-139417200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr7:139411800-139417400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr7:139412000-139416800	Strong transcription	Esophagus	oesophagus
22	chr7:139412000-139417000	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr7:139412400-139417000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr7:139412400-139420000	Weak transcription	Psoas Muscle	Psoas
25	chr7:139412600-139417400	Strong transcription	Fetal Intestine Large	intestine
26	chr7:139412600-139417400	Strong transcription	Fetal Intestine Small	intestine
27	chr7:139412800-139416800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr7:139412800-139416800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr7:139413000-139416600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr7:139413000-139417000	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr7:139413000-139417000	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr7:139413200-139417000	Strong transcription	HepG2	liver
33	chr7:139413200-139417000	Strong transcription	Osteobl	bone
34	chr7:139413200-139417400	Strong transcription	Muscle Satellite Cultured Cells	--
35	chr7:139413400-139415800	Genic enhancers	Brain Cingulate Gyrus	brain
36	chr7:139413400-139417000	Strong transcription	Thymus	Thymus
37	chr7:139413400-139417400	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr7:139413400-139417400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr7:139413600-139417000	Strong transcription	Fetal Brain Female	brain
40	chr7:139413600-139417400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr7:139413800-139416600	Strong transcription	Aorta	Aorta
42	chr7:139413800-139416800	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr7:139413800-139416800	Strong transcription	HSMMtube	muscle
44	chr7:139413800-139417000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr7:139413800-139417200	Strong transcription	Primary hematopoietic stem cells	blood
46	chr7:139414000-139417200	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr7:139414200-139417400	Strong transcription	Pancreas	Pancrea
48	chr7:139414400-139415800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr7:139414400-139416000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr7:139414400-139416800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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