Variant report

Variant	rs38019
Chromosome Location	chr7:8047683-8047684
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:8012721..8014587-chr7:8046373..8049068,2	MCF-7	breast:
2	chr7:8008115..8009822-chr7:8045668..8048452,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000106415	Chromatin interaction
ENSG00000233108	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10215645	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10226050	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.90[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10228900	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10229643	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10231036	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10241457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10243846	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10246564	0.82[CEU][hapmap]
rs10247928	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10248588	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10258788	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10273241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10486205	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11976862	0.96[YRI][hapmap]
rs11984078	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12702692	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12702693	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17568389	0.95[CHB][hapmap];0.93[JPT][hapmap];0.90[YRI][hapmap];0.81[ASN][1000 genomes]
rs2079853	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2109382	0.93[CEU][hapmap];0.93[YRI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2191321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2348774	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs258853	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28488572	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28670736	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3735457	0.82[CEU][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes]
rs37975	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs37977	1.00[CEU][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs37978	0.81[EUR][1000 genomes]
rs37981	1.00[CEU][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs37983	0.82[EUR][1000 genomes]
rs37988	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs37992	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs37994	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs37995	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs37998	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs37999	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38001	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs38002	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs38003	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs38004	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38006	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs38010	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs38011	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs38013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38014	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38016	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs38017	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38018	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs38021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs38022	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs38023	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4140809	0.85[YRI][hapmap]
rs4236406	0.96[YRI][hapmap];0.84[AMR][1000 genomes]
rs4720761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4725057	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4725060	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4725065	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs4725068	0.89[YRI][hapmap];0.81[AMR][1000 genomes]
rs62433404	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7785493	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9692283	0.93[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats 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	84 gene(s)	inside rSNPs	diseases
2	esv2752177	chr7:7729247-8177689	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv917172	chr7:7854632-8807385	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1030180	chr7:7860424-8059221	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	esv3346837	chr7:7915187-8068557	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs38019	GLCCI1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:8029800-8049000	Weak transcription	Fetal Heart	heart
2	chr7:8036400-8077400	Weak transcription	Right Ventricle	heart
3	chr7:8036600-8053800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr7:8036600-8057200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr7:8036600-8064400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr7:8036600-8064400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr7:8036600-8074600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr7:8038000-8066000	Weak transcription	Pancreas	Pancrea
9	chr7:8038400-8066000	Weak transcription	Spleen	Spleen
10	chr7:8041600-8053800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr7:8041600-8064400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr7:8041600-8095000	Weak transcription	Gastric	stomach
13	chr7:8041800-8075400	Weak transcription	Brain Hippocampus Middle	brain
14	chr7:8042800-8064400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr7:8043000-8049400	Strong transcription	Dnd41	blood
16	chr7:8043000-8050600	Strong transcription	GM12878-XiMat	blood
17	chr7:8043000-8051600	Strong transcription	Fetal Thymus	thymus
18	chr7:8043000-8099200	Weak transcription	Colon Smooth Muscle	Colon
19	chr7:8043200-8048400	Strong transcription	Hela-S3	cervix
20	chr7:8043200-8048800	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr7:8043200-8048800	Weak transcription	NHDF-Ad	bronchial
22	chr7:8043600-8048400	Strong transcription	Adipose Nuclei	Adipose
23	chr7:8043600-8048800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr7:8043600-8049400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr7:8043600-8049600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr7:8043600-8051800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr7:8043600-8052200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr7:8043600-8068400	Weak transcription	NH-A	brain
29	chr7:8043800-8048200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr7:8043800-8049600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr7:8043800-8064400	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr7:8043800-8064600	Weak transcription	Small Intestine	intestine
33	chr7:8044000-8062600	Weak transcription	Fetal Intestine Small	intestine
34	chr7:8044200-8048200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr7:8044200-8048400	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr7:8044200-8048400	Strong transcription	Thymus	Thymus
37	chr7:8044200-8051200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr7:8044200-8052000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr7:8044200-8063800	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr7:8044200-8066000	Weak transcription	Lung	lung
41	chr7:8044400-8048000	Strong transcription	Fetal Intestine Large	intestine
42	chr7:8044600-8074400	Weak transcription	Brain Angular Gyrus	brain
43	chr7:8044800-8048400	Weak transcription	NHLF	lung
44	chr7:8044800-8064400	Weak transcription	Aorta	Aorta
45	chr7:8045200-8048000	Strong transcription	Placenta	Placenta
46	chr7:8045200-8048200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr7:8045200-8066000	Weak transcription	Fetal Brain Male	brain
48	chr7:8045400-8048400	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr7:8045600-8048000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr7:8045600-8048400	Strong transcription	Liver	Liver

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