Variant report

Variant	rs3769541
Chromosome Location	chr2:33502505-33502506
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:33169785..33172664-chr2:33500827..33503324,2	K562	blood:

Variant related genes	Relation type
ENSG00000049323	Chromatin interaction
ENSG00000206951	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12987969	1.00[CHB][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1453842	0.80[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs1463311	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1463312	0.85[CHB][hapmap];0.91[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs1463313	0.85[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs1823834	0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];0.84[MEX][hapmap];0.83[MKK][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2123770	0.86[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap]
rs2887067	0.84[ASN][1000 genomes]
rs7572682	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs817530	0.86[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs817531	0.86[CHD][hapmap];0.80[MEX][hapmap]
rs817533	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][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	nsv998167	chr2:33074313-33541100	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535623	chr2:33074313-33541100	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1005435	chr2:33136117-33747159	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv535624	chr2:33136117-33747159	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
5	nsv873791	chr2:33489975-33586776	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
6	nsv518285	chr2:33502505-33509219	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3769541	SLC30A6	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:33472000-33516600	Weak transcription	Psoas Muscle	Psoas
2	chr2:33487000-33509800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr2:33490600-33515600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr2:33491800-33504400	Weak transcription	Colonic Mucosa	Colon
5	chr2:33492000-33515800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:33492200-33516600	Weak transcription	Brain Hippocampus Middle	brain
7	chr2:33492200-33516600	Weak transcription	Brain Substantia Nigra	brain
8	chr2:33492400-33547400	Weak transcription	Fetal Intestine Small	intestine
9	chr2:33492600-33508400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:33493600-33515200	Weak transcription	Fetal Lung	lung
11	chr2:33493800-33503400	Weak transcription	Fetal Brain Female	brain
12	chr2:33493800-33515400	Weak transcription	Colon Smooth Muscle	Colon
13	chr2:33494200-33506200	Weak transcription	Fetal Heart	heart
14	chr2:33494200-33516000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr2:33494200-33516200	Weak transcription	Fetal Kidney	kidney
16	chr2:33494600-33515200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr2:33497800-33503400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:33499200-33508000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:33500200-33504800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr2:33500400-33502600	Genic enhancers	Muscle Satellite Cultured Cells	--
21	chr2:33500800-33502600	Genic enhancers	Fetal Muscle Leg	muscle
22	chr2:33500800-33503800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
23	chr2:33501000-33502600	Strong transcription	Right Ventricle	heart
24	chr2:33501000-33503200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:33501000-33503200	Weak transcription	Gastric	stomach
26	chr2:33501000-33503200	Weak transcription	HMEC	breast
27	chr2:33501200-33502600	Genic enhancers	Stomach Smooth Muscle	stomach
28	chr2:33501200-33505400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:33501200-33505600	Weak transcription	NHLF	lung
30	chr2:33501200-33511000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:33501200-33516400	Weak transcription	Stomach Mucosa	stomach
32	chr2:33501200-33528800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr2:33501400-33502800	Enhancers	A549	lung
34	chr2:33501400-33503400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:33501400-33503600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:33501400-33503600	Weak transcription	HSMM	muscle
37	chr2:33501400-33516600	Weak transcription	K562	blood
38	chr2:33501600-33502600	Enhancers	Right Atrium	heart
39	chr2:33501600-33502600	Strong transcription	NHDF-Ad	bronchial
40	chr2:33501600-33503200	Enhancers	Fetal Muscle Trunk	muscle
41	chr2:33501600-33505400	Strong transcription	NH-A	brain
42	chr2:33501600-33509000	Weak transcription	HUVEC	blood vessel
43	chr2:33501800-33503800	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr2:33501800-33517800	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr2:33502000-33502600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr2:33502000-33502600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr2:33502000-33502600	Genic enhancers	Left Ventricle	heart
48	chr2:33502000-33502600	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr2:33502000-33503200	Enhancers	Ovary	ovary
50	chr2:33502000-33504200	Enhancers	Fetal Brain Male	brain

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