Variant report

Variant	rs1129156
Chromosome Location	chr19:40719076-40719077
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:40718966..40720557-chr19:40970045..40972641,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160460	Chromatin interaction
ENSG00000090013	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10402740	1.00[ASW][hapmap];0.85[CEU][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11668242	0.95[CHB][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap]
rs11880261	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap]
rs12971806	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12975651	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs189281	0.93[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2304184	0.87[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];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2304189	0.94[CHB][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2356229	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs339522	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs339523	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs339525	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs339526	0.89[ASW][hapmap];0.80[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.84[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3730050	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap]
rs3730051	0.85[CHB][hapmap];0.93[MEX][hapmap]
rs3746005	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4239504	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4257318	0.95[CHB][hapmap];0.85[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap]
rs4337402	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs4490099	0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4530264	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4558508	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap]
rs4802070	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802071	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap]
rs4802073	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs4802074	0.87[MEX][hapmap]
rs4803320	0.95[CHB][hapmap];0.85[JPT][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56694147	0.83[ASN][1000 genomes]
rs6508936	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs7247201	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7249146	0.95[CHB][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap]
rs7250897	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap]
rs7252471	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs7257972	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs7258548	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7260249	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7260517	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap]
rs8100018	0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs8102171	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap]
rs8106744	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8110888	0.95[CHB][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap]
rs969531	0.84[CHB][hapmap];0.85[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap]
rs9749056	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv2758499	chr19:40612420-40839520	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv2758761	chr19:40612420-40839520	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv911698	chr19:40689580-40725304	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv911699	chr19:40691632-40816530	Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv911700	chr19:40695598-40725304	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv911701	chr19:40695598-40728417	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv911702	chr19:40697061-40731371	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv911703	chr19:40711333-40730279	Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv911704	chr19:40716652-40730279	Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
11	nsv911705	chr19:40716652-40731371	ZNF genes & repeats Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
12	esv3371347	chr19:40717612-40722010	Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
13	nsv9727	chr19:40718313-40720726	Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
14	esv3342627	chr19:40718537-40721085	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
15	esv3391005	chr19:40718862-40721060	Weak transcription Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1129156	GRIN2D	cis	cerebellum	SCAN
rs1129156	C19orf47	cis	lymphoblastoid	seeQTL
rs1129156	IGFL4	cis	parietal	SCAN
rs1129156	ZNF229	cis	cerebellum	SCAN
rs1129156	ZNF221	cis	cerebellum	SCAN
rs1129156	SPACA4	cis	cerebellum	SCAN
rs1129156	C19orf47	cis	multi-tissue	Pritchard

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40698600-40721200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr19:40698800-40719600	Weak transcription	HSMM	muscle
3	chr19:40698800-40720200	Weak transcription	NHEK	skin
4	chr19:40698800-40721400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr19:40698800-40722000	Weak transcription	Fetal Thymus	thymus
6	chr19:40699000-40720400	Weak transcription	Psoas Muscle	Psoas
7	chr19:40699000-40722200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr19:40699000-40722200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr19:40699000-40722400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr19:40699200-40720200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr19:40699200-40720400	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr19:40699200-40721200	Weak transcription	NH-A	brain
13	chr19:40699200-40721400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr19:40699400-40721200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr19:40699600-40722000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr19:40699600-40722200	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr19:40699800-40720000	Weak transcription	NHDF-Ad	bronchial
18	chr19:40699800-40720600	Weak transcription	HepG2	liver
19	chr19:40707000-40722400	Weak transcription	HMEC	breast
20	chr19:40709800-40722000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr19:40710600-40721200	Weak transcription	Primary B cells from peripheral blood	blood
22	chr19:40710600-40722200	Weak transcription	Primary B cells from cord blood	blood
23	chr19:40711200-40721800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr19:40711200-40731800	Weak transcription	Right Atrium	heart
25	chr19:40711600-40719800	Weak transcription	Colonic Mucosa	Colon
26	chr19:40711600-40720400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr19:40711600-40721000	Weak transcription	HSMMtube	muscle
28	chr19:40711600-40721800	Weak transcription	Fetal Brain Male	brain
29	chr19:40711600-40722600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr19:40711800-40720600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr19:40712200-40720400	Strong transcription	Fetal Stomach	stomach
32	chr19:40712200-40722400	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr19:40712200-40722600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr19:40712200-40722600	Weak transcription	Esophagus	oesophagus
35	chr19:40713200-40719200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr19:40713200-40725200	Weak transcription	Hela-S3	cervix
37	chr19:40714000-40720800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr19:40714200-40722000	Strong transcription	Brain Germinal Matrix	brain
39	chr19:40714400-40720800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr19:40714600-40719200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr19:40714600-40719200	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr19:40714600-40719400	Strong transcription	Fetal Intestine Small	intestine
43	chr19:40714600-40720600	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr19:40714600-40720800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr19:40714600-40720800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr19:40714800-40719200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr19:40714800-40719400	Strong transcription	Fetal Muscle Trunk	muscle
48	chr19:40714800-40720600	Strong transcription	Brain Anterior Caudate	brain
49	chr19:40714800-40721000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr19:40714800-40721200	Strong transcription	Brain Hippocampus Middle	brain

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