Variant report

Variant	rs38017
Chromosome Location	chr7:8046062-8046063
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:8043881..8046196-chr7:8058398..8061346,2	MCF-7	breast:
2	chr7:8008115..8009822-chr7:8045668..8048452,4	MCF-7	breast:
3	chr7:8009215..8011619-chr7:8044493..8047371,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233108	Chromatin interaction
ENSG00000106415	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10215645	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10226050	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10228900	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10229643	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10231036	0.87[AMR][1000 genomes]
rs10241457	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10243846	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10247928	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10248588	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10258788	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10273241	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10486205	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11984078	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12702692	0.84[ASN][1000 genomes]
rs12702693	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17568389	0.81[ASN][1000 genomes]
rs2079853	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2109382	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2191321	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2348774	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs258853	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28488572	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28670736	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs37975	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs37977	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs37978	0.85[EUR][1000 genomes]
rs37981	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs37983	0.85[EUR][1000 genomes]
rs37988	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs37992	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs37994	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs37995	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs37998	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs37999	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38001	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs38002	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs38003	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs38004	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38006	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs38010	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs38011	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38012	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs38013	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38014	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38016	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs38018	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs38019	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38021	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs38022	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs38023	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4236406	0.80[AMR][1000 genomes]
rs4720761	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4725057	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4725060	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62433404	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7785493	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9692283	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
6	nsv1020161	chr7:7929384-8047553	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	esv1796855	chr7:8042555-8047169	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs38017	GLCCI1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:8029800-8046400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr7:8029800-8049000	Weak transcription	Fetal Heart	heart
3	chr7:8036400-8046600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr7:8036400-8077400	Weak transcription	Right Ventricle	heart
5	chr7:8036600-8053800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr7:8036600-8057200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr7:8036600-8064400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr7:8036600-8064400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr7:8036600-8074600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr7:8036800-8046400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr7:8038000-8066000	Weak transcription	Pancreas	Pancrea
12	chr7:8038400-8046400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr7:8038400-8066000	Weak transcription	Spleen	Spleen
14	chr7:8039400-8046400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr7:8039400-8046400	Weak transcription	Left Ventricle	heart
16	chr7:8039400-8046400	Weak transcription	Ovary	ovary
17	chr7:8040000-8046400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr7:8041200-8046400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr7:8041600-8046400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr7:8041600-8053800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr7:8041600-8064400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr7:8041600-8095000	Weak transcription	Gastric	stomach
23	chr7:8041800-8075400	Weak transcription	Brain Hippocampus Middle	brain
24	chr7:8042400-8046400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr7:8042800-8046800	Strong transcription	Primary hematopoietic stem cells	blood
26	chr7:8042800-8047200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr7:8042800-8064400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr7:8043000-8046400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr7:8043000-8046400	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr7:8043000-8049400	Strong transcription	Dnd41	blood
31	chr7:8043000-8050600	Strong transcription	GM12878-XiMat	blood
32	chr7:8043000-8051600	Strong transcription	Fetal Thymus	thymus
33	chr7:8043000-8099200	Weak transcription	Colon Smooth Muscle	Colon
34	chr7:8043200-8048400	Strong transcription	Hela-S3	cervix
35	chr7:8043200-8048800	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr7:8043200-8048800	Weak transcription	NHDF-Ad	bronchial
37	chr7:8043400-8047600	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr7:8043600-8047200	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr7:8043600-8047200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr7:8043600-8047400	Strong transcription	Primary B cells from cord blood	blood
41	chr7:8043600-8048400	Strong transcription	Adipose Nuclei	Adipose
42	chr7:8043600-8048800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr7:8043600-8049400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr7:8043600-8049600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr7:8043600-8051800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr7:8043600-8052200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr7:8043600-8068400	Weak transcription	NH-A	brain
48	chr7:8043800-8047200	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr7:8043800-8047200	Strong transcription	Fetal Lung	lung
50	chr7:8043800-8047400	Strong transcription	HUES64 Cell Line	embryonic stem cell

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