Variant report

Variant	rs7617405
Chromosome Location	chr3:98612778-98612779
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:98602528..98604913-chr3:98611525..98613667,2	K562	blood:
2	chr3:98612045..98613776-chr3:98618564..98620858,2	MCF-7	breast:
3	chr3:98610185..98614055-chr3:98618710..98621878,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000239462	Chromatin interaction
ENSG00000057019	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs278384	1.00[CHD][hapmap]
rs62276868	0.81[EUR][1000 genomes]
rs62278488	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62278535	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62278540	0.90[EUR][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	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7617405	SDC4	trans	lymphoblastoid	seeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98593800-98619400	Weak transcription	Small Intestine	intestine
2	chr3:98594400-98616600	Weak transcription	Fetal Brain Male	brain
3	chr3:98597400-98619000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr3:98599800-98618400	Weak transcription	Fetal Brain Female	brain
5	chr3:98600600-98613000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:98600600-98618000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr3:98600600-98618000	Weak transcription	Fetal Thymus	thymus
8	chr3:98602200-98613600	Genic enhancers	HSMM	muscle
9	chr3:98602400-98613600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:98604000-98613000	Enhancers	NHLF	lung
11	chr3:98604400-98614600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:98605000-98618600	Weak transcription	Fetal Stomach	stomach
13	chr3:98606400-98618400	Weak transcription	Fetal Kidney	kidney
14	chr3:98606600-98618000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:98608800-98614400	Enhancers	K562	blood
16	chr3:98609000-98612800	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr3:98609000-98613200	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr3:98609000-98615800	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr3:98609200-98613400	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr3:98609400-98613400	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr3:98609400-98613800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:98609600-98613400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:98609800-98613800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr3:98609800-98614200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:98610000-98612800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr3:98610400-98615000	Transcr. at gene 5' and 3'	Osteobl	bone
27	chr3:98610400-98615800	Transcr. at gene 5' and 3'	NH-A	brain
28	chr3:98610400-98616600	Transcr. at gene 5' and 3'	A549	lung
29	chr3:98610600-98613400	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr3:98610800-98614200	Enhancers	Right Ventricle	heart
31	chr3:98610800-98618400	Weak transcription	Brain Anterior Caudate	brain
32	chr3:98610800-98618400	Enhancers	Fetal Heart	heart
33	chr3:98610800-98618600	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:98611000-98613200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:98611000-98613200	Enhancers	HepG2	liver
36	chr3:98611200-98613400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr3:98611200-98617000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr3:98611400-98612800	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr3:98611400-98618800	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr3:98611400-98619200	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr3:98611600-98613000	Enhancers	Adipose Nuclei	Adipose
42	chr3:98611600-98616600	Weak transcription	Fetal Lung	lung
43	chr3:98611800-98612800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr3:98611800-98613200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr3:98611800-98613400	Genic enhancers	HUVEC	blood vessel
46	chr3:98611800-98618400	Weak transcription	Colon Smooth Muscle	Colon
47	chr3:98611800-98618600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr3:98612000-98612800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr3:98612000-98612800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr3:98612000-98612800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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