Variant report

Variant	rs3007673
Chromosome Location	chr1:152002188-152002189
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:152001004..152003518-chr1:152088501..152090154,2	MCF-7	breast:
2	chr1:151958520..151979218-chr1:151992734..152014750,97	MCF-7	breast:
3	chr1:151906991..151909574-chr1:152001582..152003967,2	K562	blood:
4	chr1:151896761..151899276-chr1:152001474..152003211,2	MCF-7	breast:
5	chr1:151798310..151800622-chr1:152001051..152003232,2	K562	blood:

Variant related genes	Relation type
ENSG00000197747	Chromatin interaction
ENSG00000229021	Chromatin interaction
ENSG00000143365	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1496037	0.95[ASN][1000 genomes]
rs2999547	0.87[ASN][1000 genomes]
rs2999551	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2999552	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999553	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2999554	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2999555	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2999562	1.00[ASN][1000 genomes]
rs3007672	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3007676	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3007677	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3007678	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3007679	0.87[EUR][1000 genomes]
rs3104205	0.81[ASN][1000 genomes]
rs3122300	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3122301	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3122302	0.90[EUR][1000 genomes]
rs3122303	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3122304	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3134814	0.85[AFR][1000 genomes]
rs3811422	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	191 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3007673	S100A11	Cis_1M	lymphoblastoid	RTeQTL
rs3007673	LOC729659///LOC730278	trans	lymphoblastoid	RTeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151986800-152007400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:151988600-152002600	Weak transcription	Fetal Muscle Leg	muscle
3	chr1:151988600-152004000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:151993400-152003000	Weak transcription	Fetal Intestine Small	intestine
5	chr1:151994000-152002400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:151994400-152003200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:151996600-152004400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:151996800-152004000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:151997000-152003400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:151997000-152004200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr1:151997000-152004400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:151997000-152004800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:151997000-152006600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:151997000-152007000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:151997800-152003200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:151997800-152003400	Weak transcription	Lung	lung
17	chr1:151998600-152003000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:151998800-152002800	Enhancers	HMEC	breast
19	chr1:151999000-152004200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr1:151999200-152002600	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr1:151999200-152002600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:151999400-152004000	Weak transcription	Aorta	Aorta
23	chr1:151999600-152003400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr1:151999600-152003400	Weak transcription	NH-A	brain
25	chr1:151999800-152002600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr1:152000000-152004000	Weak transcription	NHLF	lung
27	chr1:152000200-152005000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:152000400-152004200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr1:152000400-152004600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr1:152000600-152003000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr1:152000600-152003200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:152000600-152003400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr1:152000800-152002600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr1:152000800-152002600	Weak transcription	Fetal Thymus	thymus
35	chr1:152000800-152003400	Weak transcription	Fetal Intestine Large	intestine
36	chr1:152000800-152003600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr1:152000800-152004000	Weak transcription	Fetal Kidney	kidney
38	chr1:152001000-152002800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:152001000-152003200	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr1:152001000-152003200	Enhancers	Dnd41	blood
41	chr1:152001000-152003200	Weak transcription	HUVEC	blood vessel
42	chr1:152001200-152002200	Enhancers	Placenta	Placenta
43	chr1:152001200-152002600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:152001200-152002800	Enhancers	Adipose Nuclei	Adipose
45	chr1:152001200-152003000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:152001200-152004000	Weak transcription	Fetal Lung	lung
47	chr1:152001200-152004600	Weak transcription	Spleen	Spleen
48	chr1:152001400-152002400	Enhancers	Osteobl	bone
49	chr1:152001400-152002800	Enhancers	NHDF-Ad	bronchial
50	chr1:152001400-152003000	Enhancers	Hela-S3	cervix

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