Variant report

Variant	rs37990
Chromosome Location	chr7:8027174-8027175
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:8026444..8027944-chr7:8028522..8030290,2	MCF-7	breast:
2	chr7:8007372..8010474-chr7:8024830..8028322,4	MCF-7	breast:
3	chr7:8024866..8028296-chr7:8029359..8032813,3	K562	blood:
4	chr7:8016338..8018811-chr7:8026553..8029436,2	MCF-7	breast:
5	chr7:8008849..8010688-chr7:8026210..8029126,2	K562	blood:
6	chr7:8007272..8010688-chr7:8026210..8029126,4	K562	blood:
7	chr7:8008267..8010866-chr7:8026325..8028271,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233108	Chromatin interaction
ENSG00000106415	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10253260	0.92[CEU][hapmap];0.81[AMR][1000 genomes]
rs10257285	0.92[CEU][hapmap]
rs10265283	0.92[CEU][hapmap]
rs10272512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2159510	0.82[AMR][1000 genomes]
rs28177	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35953256	0.82[AMR][1000 genomes]
rs37984	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs37985	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs37991	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs38005	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4725058	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4725063	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4725066	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs4725069	0.92[CEU][hapmap]
rs6463754	0.82[AMR][1000 genomes]
rs6463755	0.92[CEU][hapmap];0.82[AMR][1000 genomes]
rs6943211	0.81[EUR][1000 genomes]
rs6974264	0.92[CEU][hapmap]
rs6975078	0.96[CEU][hapmap];0.81[AMR][1000 genomes]
rs7795506	0.88[CEU][hapmap]
rs7798367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7806440	0.83[AMR][1000 genomes]
rs929509	0.95[CEU][hapmap];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs37990	GLCCI1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:8013400-8029000	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr7:8013400-8029600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr7:8014200-8028600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr7:8015000-8045000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr7:8015200-8031800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr7:8016600-8027200	Weak transcription	Fetal Thymus	thymus
7	chr7:8017800-8029000	Weak transcription	Hela-S3	cervix
8	chr7:8017800-8029600	Weak transcription	Colon Smooth Muscle	Colon
9	chr7:8017800-8029600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr7:8018000-8029000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr7:8019000-8031400	Weak transcription	Primary B cells from cord blood	blood
12	chr7:8019600-8029400	Weak transcription	Adipose Nuclei	Adipose
13	chr7:8020000-8027600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr7:8020400-8028200	Weak transcription	Fetal Heart	heart
15	chr7:8021600-8029000	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr7:8022000-8028800	Weak transcription	Brain Germinal Matrix	brain
17	chr7:8023800-8028400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr7:8024000-8027200	Weak transcription	Psoas Muscle	Psoas
19	chr7:8024000-8028800	Weak transcription	Small Intestine	intestine
20	chr7:8024000-8029200	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr7:8025000-8029600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr7:8025000-8031600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:8025200-8028400	Weak transcription	Liver	Liver
24	chr7:8025200-8029000	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr7:8025200-8029200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr7:8026000-8027800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr7:8026000-8028600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr7:8026000-8028600	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr7:8026200-8027200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr7:8026400-8029200	Enhancers	K562	blood
31	chr7:8026400-8031000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr7:8026600-8029000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr7:8026600-8029000	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr7:8026600-8029400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr7:8026600-8029400	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr7:8026800-8027800	Genic enhancers	GM12878-XiMat	blood
37	chr7:8026800-8028600	Enhancers	Primary T cells from cord blood	blood
38	chr7:8026800-8028800	Enhancers	Dnd41	blood
39	chr7:8026800-8029000	Enhancers	Thymus	Thymus

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