Variant report

Variant	rs11642770
Chromosome Location	chr16:70749970-70749971
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:70748062..70750607-chr16:70762879..70765510,3	MCF-7	breast:
2	chr16:70710236..70712710-chr16:70749710..70751243,2	K562	blood:
3	chr16:70740784..70746452-chr16:70747278..70752169,9	K562	blood:
4	chr16:70748104..70753433-chr16:70779056..70781695,7	MCF-7	breast:
5	chr16:70747047..70751292-chr16:70770500..70773277,5	MCF-7	breast:
6	chr16:70748975..70750633-chr16:70770017..70771781,2	MCF-7	breast:
7	chr16:70749284..70751657-chr16:70760367..70762394,2	MCF-7	breast:
8	chr16:70747966..70750643-chr16:70785979..70788271,2	MCF-7	breast:
9	chr16:70747788..70750728-chr16:70794954..70796850,2	MCF-7	breast:
10	chr16:70747879..70752178-chr16:70754716..70759017,5	MCF-7	breast:
11	chr16:70719656..70721781-chr16:70748712..70752057,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000260156	Chromatin interaction
ENSG00000103043	Chromatin interaction
ENSG00000132613	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11075781	0.85[YRI][hapmap]
rs11640251	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11641739	0.93[ASN][1000 genomes]
rs11642775	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11649305	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1551527	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2242126	0.94[ASW][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs2278984	0.83[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs4985419	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4985563	0.94[ASW][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs8048078	0.87[GIH][hapmap];0.87[JPT][hapmap]
rs8054653	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8059238	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs936301	0.87[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs936302	0.89[CHB][hapmap];0.89[YRI][hapmap];0.91[ASN][1000 genomes]
rs9673700	0.85[AFR][1000 genomes]
rs9934869	0.85[GIH][hapmap];0.85[JPT][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs9935596	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv517391	chr16:70666410-70840490	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer 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	30 gene(s)	inside rSNPs	diseases
2	nsv457517	chr16:70666722-70840490	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv572945	chr16:70666722-70840490	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv906876	chr16:70677785-70757555	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv906877	chr16:70677785-70766378	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats 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	18 gene(s)	inside rSNPs	diseases
6	nsv906878	chr16:70677785-70782922	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv906879	chr16:70677785-70790831	Flanking Active TSS Weak transcription Enhancers Strong transcription 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	19 gene(s)	inside rSNPs	diseases
8	nsv906880	chr16:70677785-70796515	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv471094	chr16:70694000-70749970	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
10	nsv1059226	chr16:70708698-70779144	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
11	nsv906889	chr16:70724001-70790831	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv906890	chr16:70740707-70790831	Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11642770	TMED6	cis	cerebellum	SCAN
rs11642770	EXOC3L	cis	cerebellum	SCAN
rs11642770	IL34	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:70720400-70753200	Weak transcription	Primary B cells from cord blood	blood
2	chr16:70727000-70770800	Weak transcription	GM12878-XiMat	blood
3	chr16:70731400-70755000	Weak transcription	Small Intestine	intestine
4	chr16:70733200-70759400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr16:70733400-70754000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr16:70733800-70753400	Weak transcription	Dnd41	blood
7	chr16:70734600-70751200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr16:70737000-70753800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr16:70741000-70752800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr16:70741400-70753400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr16:70742400-70751200	Enhancers	Brain Hippocampus Middle	brain
12	chr16:70742400-70752600	Weak transcription	Hela-S3	cervix
13	chr16:70744000-70754800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr16:70744200-70750400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr16:70744200-70750800	Enhancers	Fetal Thymus	thymus
16	chr16:70744200-70752600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr16:70744400-70752600	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr16:70744400-70752600	Weak transcription	Duodenum Mucosa	Duodenum
19	chr16:70744400-70753000	Enhancers	Fetal Muscle Leg	muscle
20	chr16:70744400-70754000	Weak transcription	Aorta	Aorta
21	chr16:70744800-70750800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr16:70744800-70751400	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr16:70745000-70751000	Enhancers	Fetal Heart	heart
24	chr16:70745000-70751200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr16:70745200-70750200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr16:70745200-70750400	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr16:70745200-70751000	Enhancers	Rectal Smooth Muscle	rectum
28	chr16:70745200-70753600	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr16:70745400-70750400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr16:70745400-70753200	Enhancers	Placenta	Placenta
31	chr16:70745600-70750200	Weak transcription	Gastric	stomach
32	chr16:70745600-70750200	Enhancers	Thymus	Thymus
33	chr16:70745800-70750200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr16:70745800-70750400	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr16:70746000-70750600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr16:70746000-70750800	Enhancers	HepG2	liver
37	chr16:70746400-70752000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr16:70746400-70752000	Enhancers	Brain Cingulate Gyrus	brain
39	chr16:70746600-70750000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr16:70746800-70753200	Weak transcription	Primary T cells from cord blood	blood
41	chr16:70747000-70750400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr16:70747000-70751000	Enhancers	NHDF-Ad	bronchial
43	chr16:70747000-70751000	Enhancers	NHLF	lung
44	chr16:70747000-70751200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr16:70747200-70750200	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr16:70747200-70750400	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr16:70747200-70751200	Enhancers	Right Ventricle	heart
48	chr16:70747400-70750400	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr16:70747400-70753400	Weak transcription	Primary B cells from peripheral blood	blood
50	chr16:70747800-70750400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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