Variant report

Variant	rs816411
Chromosome Location	chr7:56171489-56171490
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:4566915..4567444-chr7:56171158..56171772,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10255049	0.84[ASN][1000 genomes]
rs10258800	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11238394	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11773374	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11773453	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12537943	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13234899	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13242830	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13244654	0.89[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.84[LWK][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1894832	0.85[CEU][hapmap];0.87[AMR][1000 genomes]
rs2002651	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2016482	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2016724	0.88[CEU][hapmap];0.80[AMR][1000 genomes]
rs2242508	0.81[CHB][hapmap];0.83[CHD][hapmap];0.81[LWK][hapmap]
rs2331180	0.84[CEU][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2538047	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2908543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2908544	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2908545	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2908550	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4275190	0.81[CHB][hapmap]
rs4947536	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4948106	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6593297	0.81[CHB][hapmap]
rs6945795	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7782243	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7783339	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7793921	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7799471	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7801169	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs816408	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs816409	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs860118	0.84[CEU][hapmap]
rs933466	0.85[CEU][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9767946	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829874	chr7:55382925-56369816	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv995105	chr7:55606107-56174888	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	esv12412	chr7:55619800-56385412	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv949574	chr7:55705566-56544711	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	esv3446617	chr7:55745934-56485903	Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
6	nsv529162	chr7:55800753-56174888	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	esv2761334	chr7:55823581-56424739	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
8	nsv1018806	chr7:55844931-56383936	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv538860	chr7:55844931-56383936	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
10	nsv498114	chr7:55872850-56174888	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
11	nsv1034712	chr7:56146885-56605592	Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
12	nsv538861	chr7:56146885-56605592	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
13	nsv970483	chr7:56169231-56172955	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	nsv526294	chr7:56171489-56622630	Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs816411	SUMF2	cis	parietal	SCAN
rs816411	CHCHD2	cis	parietal	SCAN
rs816411	CHCHD2	cis	multi-tissue	Pritchard
rs816411	CHCHD2	cis	cerebellum	SCAN
rs816411	SUMF2	cis	cerebellum	SCAN
rs816411	GBAS	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56158200-56173200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:56161000-56173000	Weak transcription	Fetal Heart	heart
3	chr7:56161200-56173000	Weak transcription	Right Atrium	heart
4	chr7:56164000-56172800	Strong transcription	Fetal Stomach	stomach
5	chr7:56164200-56171600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr7:56164200-56172000	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr7:56164200-56172600	Strong transcription	Fetal Intestine Small	intestine
8	chr7:56165000-56172200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr7:56165200-56172000	Strong transcription	Fetal Brain Female	brain
10	chr7:56165200-56172800	Strong transcription	Thymus	Thymus
11	chr7:56165400-56172000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr7:56165400-56172200	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr7:56165400-56172200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr7:56165400-56172400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr7:56166000-56171800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr7:56166200-56172200	Strong transcription	Fetal Intestine Large	intestine
17	chr7:56166200-56172200	Strong transcription	Fetal Thymus	thymus
18	chr7:56166200-56172600	Strong transcription	Fetal Muscle Leg	muscle
19	chr7:56166400-56172200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr7:56166800-56171600	Strong transcription	Colon Smooth Muscle	Colon
21	chr7:56166800-56171600	Strong transcription	Skeletal Muscle Female	skeletal muscle
22	chr7:56166800-56171800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr7:56166800-56172000	Strong transcription	Lung	lung
24	chr7:56167000-56171800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr7:56167000-56171800	Strong transcription	Stomach Smooth Muscle	stomach
26	chr7:56167000-56172000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr7:56167000-56172000	Strong transcription	Primary B cells from cord blood	blood
28	chr7:56167000-56172000	Strong transcription	Primary T cells from cord blood	blood
29	chr7:56167000-56172000	Strong transcription	Duodenum Mucosa	Duodenum
30	chr7:56167000-56172000	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr7:56167000-56172000	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr7:56167000-56172000	Strong transcription	Skeletal Muscle Male	skeletal muscle
33	chr7:56167000-56172200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr7:56167000-56172200	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr7:56167000-56172200	Strong transcription	Ovary	ovary
36	chr7:56167000-56172200	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr7:56167000-56172600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr7:56167000-56172800	Strong transcription	A549	lung
39	chr7:56167000-56173200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr7:56167200-56171600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr7:56167200-56171800	Strong transcription	HMEC	breast
42	chr7:56167200-56172000	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr7:56167200-56172000	Strong transcription	Primary B cells from peripheral blood	blood
44	chr7:56167200-56172000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr7:56167200-56172000	Strong transcription	Liver	Liver
46	chr7:56167200-56172000	Strong transcription	Brain Substantia Nigra	brain
47	chr7:56167200-56172000	Strong transcription	HSMMtube	muscle
48	chr7:56167200-56172000	Strong transcription	NH-A	brain
49	chr7:56167200-56172200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr7:56167200-56172200	Strong transcription	Primary monocytes fromperipheralblood	blood

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