Variant report

Variant	rs7171
Chromosome Location	chr19:41097276-41097277
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:41097212-41097563	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:41097245-41097435	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:41083044..41086167-chr19:41095673..41098202,4	K562	blood:
2	chr19:41084074..41087113-chr19:41095673..41098662,4	K562	blood:
3	chr19:41093850..41097927-chr19:41099715..41103880,5	K562	blood:
4	chr19:41091186..41093706-chr19:41096720..41098701,2	K562	blood:

Variant related genes	Relation type
LTBP4	TF binding region
ENSG00000160410	Chromatin interaction
ENSG00000090006	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10402698	0.93[ASN][1000 genomes]
rs10403467	0.85[ASN][1000 genomes]
rs10403833	0.86[ASN][1000 genomes]
rs10403963	0.85[ASN][1000 genomes]
rs10405930	0.88[ASN][1000 genomes]
rs10410606	0.88[ASN][1000 genomes]
rs1051303	0.85[ASN][1000 genomes]
rs11083561	0.89[ASN][1000 genomes]
rs1131620	0.85[ASN][1000 genomes]
rs11667706	0.85[ASN][1000 genomes]
rs11667772	0.85[ASN][1000 genomes]
rs12611045	0.85[ASN][1000 genomes]
rs12980111	0.86[ASN][1000 genomes]
rs1318544	0.88[ASN][1000 genomes]
rs1864074	0.88[ASN][1000 genomes]
rs1864078	0.88[ASN][1000 genomes]
rs1869712	0.88[ASN][1000 genomes]
rs2278246	0.85[ASN][1000 genomes]
rs2303727	0.87[ASN][1000 genomes]
rs2303729	0.88[ASN][1000 genomes]
rs2369006	0.86[ASN][1000 genomes]
rs2604902	0.88[ASN][1000 genomes]
rs28649715	0.85[ASN][1000 genomes]
rs28655571	0.86[ASN][1000 genomes]
rs392726	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs393569	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs396118	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs404584	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs406133	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs410101	0.88[ASN][1000 genomes]
rs413901	0.88[ASN][1000 genomes]
rs415075	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs420490	0.84[ASN][1000 genomes]
rs420720	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4803348	0.85[ASN][1000 genomes]
rs56353506	0.85[ASN][1000 genomes]
rs7259067	0.86[ASN][1000 genomes]
rs7259237	0.86[ASN][1000 genomes]
rs7259554	0.86[ASN][1000 genomes]
rs8107014	0.85[ASN][1000 genomes]
rs919307	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer 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 miRNA target site	139 gene(s)	inside rSNPs	diseases
2	nsv911714	chr19:41006426-41165252	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv911715	chr19:41014922-41141434	Bivalent Enhancer Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv1057634	chr19:41019512-41174259	Enhancers Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv911716	chr19:41023511-41109456	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv911717	chr19:41023511-41141434	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv911719	chr19:41033109-41147087	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
8	nsv911720	chr19:41033109-41156940	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv911721	chr19:41040334-41124931	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
10	nsv911722	chr19:41040334-41176403	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
11	nsv911723	chr19:41075990-41195279	Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
12	nsv869561	chr19:41077513-41139834	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
13	nsv1064699	chr19:41086506-41174259	Genic enhancers Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
14	nsv911724	chr19:41089505-41165252	Bivalent/Poised TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
15	nsv911725	chr19:41090190-41114065	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
16	nsv911726	chr19:41090190-41141434	Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7171	ENSG00000160410	cis	multi-tissue	Pritchard
rs7171	SHKBP1	Cis_1M	lymphoblastoid	RTeQTL
rs7171	SHKBP1	cis	Whole Blood	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41083600-41100400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr19:41083600-41101000	Weak transcription	HSMMtube	muscle
3	chr19:41084000-41097600	Strong transcription	Fetal Stomach	stomach
4	chr19:41084200-41099800	Weak transcription	Fetal Brain Male	brain
5	chr19:41084400-41100000	Weak transcription	Stomach Mucosa	stomach
6	chr19:41084600-41097600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr19:41084600-41100400	Weak transcription	NHDF-Ad	bronchial
8	chr19:41084600-41102600	Weak transcription	Right Atrium	heart
9	chr19:41084800-41097600	Strong transcription	Thymus	Thymus
10	chr19:41086000-41097800	Strong transcription	Primary T cells from cord blood	blood
11	chr19:41086400-41100400	Weak transcription	K562	blood
12	chr19:41086600-41097400	Strong transcription	Primary B cells from peripheral blood	blood
13	chr19:41086800-41097400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr19:41086800-41097400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr19:41086800-41099000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr19:41086800-41100000	Weak transcription	Fetal Brain Female	brain
17	chr19:41086800-41100600	Weak transcription	Brain Angular Gyrus	brain
18	chr19:41087200-41100400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr19:41087600-41102600	Weak transcription	Small Intestine	intestine
20	chr19:41087800-41098200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr19:41087800-41100000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr19:41088400-41100200	Weak transcription	Brain Substantia Nigra	brain
23	chr19:41088600-41100200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr19:41089200-41100400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr19:41089400-41098200	Weak transcription	Brain Germinal Matrix	brain
26	chr19:41090600-41099600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr19:41090800-41100000	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr19:41091400-41100000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr19:41092400-41097400	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr19:41092600-41097400	Strong transcription	Lung	lung
31	chr19:41092600-41097400	Strong transcription	Spleen	Spleen
32	chr19:41092600-41097600	Strong transcription	Placenta	Placenta
33	chr19:41093000-41097600	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr19:41093000-41099400	Weak transcription	Colon Smooth Muscle	Colon
35	chr19:41093200-41097400	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr19:41093200-41097800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr19:41093200-41098400	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr19:41093200-41099800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr19:41093200-41100000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr19:41093200-41100400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr19:41093400-41098000	Weak transcription	Primary hematopoietic stem cells	blood
42	chr19:41093400-41100400	Weak transcription	Brain Hippocampus Middle	brain
43	chr19:41093600-41100200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr19:41094000-41099800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr19:41094400-41100200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr19:41094400-41102400	Weak transcription	Fetal Lung	lung
47	chr19:41094600-41100400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr19:41094600-41100400	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr19:41094600-41101200	Weak transcription	Primary B cells from cord blood	blood
50	chr19:41094600-41102800	Weak transcription	Aorta	Aorta

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