Variant report

Variant	rs3800316
Chromosome Location	chr6:27256102-27256103
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27254642..27256406-chr6:27762227..27764369,2	K562	blood:
2	chr6:27255029..27257456-chr6:27262507..27264289,2	MCF-7	breast:
3	chr6:27254367..27256212-chr6:27263059..27265882,2	MCF-7	breast:
4	chr6:27255044..27257827-chr6:27773211..27776006,2	K562	blood:
5	chr6:27101409..27103867-chr6:27254948..27256808,2	K562	blood:
6	chr6:27115708..27117818-chr6:27254762..27257990,3	K562	blood:
7	chr6:27115418..27117818-chr6:27255558..27257990,3	K562	blood:

Variant related genes	Relation type
ENSG00000185130	Chromatin interaction
ENSG00000217862	Chromatin interaction
ENSG00000196747	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1102568	1.00[CHB][hapmap]
rs11753483	1.00[CHB][hapmap]
rs11755662	1.00[JPT][hapmap]
rs11965377	1.00[CHB][hapmap]
rs11966985	1.00[CHB][hapmap]
rs11967073	1.00[CHB][hapmap]
rs11968996	1.00[JPT][hapmap]
rs11969536	1.00[CHB][hapmap]
rs11970095	1.00[CHB][hapmap]
rs11970261	1.00[CHB][hapmap]
rs12664426	1.00[JPT][hapmap]
rs13211166	1.00[JPT][hapmap]
rs13217239	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs16897515	1.00[JPT][hapmap]
rs2893910	1.00[JPT][hapmap]
rs2893912	1.00[CHB][hapmap]
rs35454259	0.88[EUR][1000 genomes]
rs3800318	1.00[JPT][hapmap]
rs3823427	0.85[EUR][1000 genomes]
rs6921711	1.00[JPT][hapmap]
rs6932590	0.88[EUR][1000 genomes]
rs6938200	1.00[JPT][hapmap]
rs7744248	1.00[CHB][hapmap]
rs7746199	1.00[JPT][hapmap]
rs7759741	1.00[CHB][hapmap]
rs7760931	1.00[JPT][hapmap]
rs9969094	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1017328	chr6:27177147-27369588	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv883505	chr6:27210614-27300580	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3800316	BTN3A2	cis	lymphoblastoid	seeQTL
rs3800316	HIST1H2BH	cis	cerebellum	SCAN
rs3800316	HIST1H4L	cis	cerebellum	SCAN
rs3800316	FKSG83	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27254400-27258000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr6:27255200-27257000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:27255200-27257200	Active TSS	A549	lung
4	chr6:27255400-27256600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr6:27255400-27256600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
6	chr6:27255400-27256800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
7	chr6:27255400-27256800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr6:27255400-27257000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr6:27255400-27257000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
10	chr6:27255600-27256400	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr6:27255600-27256600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
12	chr6:27255600-27256600	Bivalent/Poised TSS	Osteobl	bone
13	chr6:27255600-27256800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:27255600-27256800	Active TSS	H9 Cell Line	embryonic stem cell
15	chr6:27255600-27256800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr6:27255600-27256800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:27255600-27256800	Active TSS	GM12878-XiMat	blood
18	chr6:27255600-27257000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
19	chr6:27255600-27257000	Flanking Bivalent TSS/Enh	NHEK	skin
20	chr6:27255800-27256200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr6:27255800-27256200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:27255800-27256200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:27255800-27256200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:27255800-27256400	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:27255800-27256400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
26	chr6:27255800-27256400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
27	chr6:27255800-27256400	Flanking Bivalent TSS/Enh	HepG2	liver
28	chr6:27255800-27256400	Bivalent/Poised TSS	HSMMtube	muscle
29	chr6:27255800-27256600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
30	chr6:27255800-27256600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:27255800-27256600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:27255800-27256600	Bivalent/Poised TSS	Placenta	Placenta
33	chr6:27255800-27256800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr6:27255800-27256800	Bivalent/Poised TSS	HSMM	muscle
35	chr6:27256000-27256200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr6:27256000-27256200	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:27256000-27256200	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr6:27256000-27256200	Bivalent/Poised TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr6:27256000-27256200	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:27256000-27256200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:27256000-27256200	Active TSS	HMEC	breast
42	chr6:27256000-27256200	Active TSS	K562	blood
43	chr6:27256000-27256400	Bivalent/Poised TSS	Primary hematopoietic stem cells short term culture	blood
44	chr6:27256000-27256400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr6:27256000-27256400	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
46	chr6:27256000-27256400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
47	chr6:27256000-27256400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr6:27256000-27256400	Bivalent Enhancer	Fetal Muscle Leg	muscle
49	chr6:27256000-27256400	Bivalent Enhancer	Left Ventricle	heart
50	chr6:27256000-27256600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived

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