Variant report

Variant	rs10993842
Chromosome Location	chr9:136749710-136749711
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:136747124..136749714-chr9:136809806..136812182,3	MCF-7	breast:
2	chr9:136748034..136750823-chr9:136772544..136775490,4	MCF-7	breast:
3	chr9:136744004..136756386-chr9:136850728..136860313,29	MCF-7	breast:
4	chr9:136711485..136713454-chr9:136747435..136749712,2	K562	blood:
5	chr9:136748871..136750946-chr9:136835211..136836752,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160293	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10821533	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12001216	0.84[CEU][hapmap]
rs12002290	0.94[CEU][hapmap];0.96[ASN][1000 genomes]
rs12002767	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3780739	0.81[EUR][1000 genomes]
rs3780741	0.81[LWK][hapmap]
rs3858104	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7852459	0.83[CEU][hapmap];0.88[ASN][1000 genomes]
rs7869522	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894114	chr9:136538798-136779153	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv831745	chr9:136593702-136780273	Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv831746	chr9:136607829-136750740	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv894122	chr9:136632662-136760639	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1035272	chr9:136665308-136772256	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv894123	chr9:136682408-136852501	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv894124	chr9:136716399-136870787	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv894125	chr9:136723520-136931957	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv894126	chr9:136747832-136779153	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv894127	chr9:136747832-136811772	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10993842	LCN8	cis	parietal	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136729600-136780000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr9:136729800-136762600	Weak transcription	Right Ventricle	heart
3	chr9:136736000-136760000	Weak transcription	Primary B cells from cord blood	blood
4	chr9:136736800-136756200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:136740000-136754800	Weak transcription	Osteobl	bone
6	chr9:136740200-136757400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr9:136741800-136753000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr9:136741800-136753200	Weak transcription	A549	lung
9	chr9:136744000-136755200	Enhancers	Fetal Muscle Leg	muscle
10	chr9:136744400-136751200	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr9:136744600-136751600	Weak transcription	Fetal Intestine Large	intestine
12	chr9:136744600-136751800	Weak transcription	GM12878-XiMat	blood
13	chr9:136744600-136753000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr9:136745600-136754600	Weak transcription	Hela-S3	cervix
15	chr9:136745800-136755600	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr9:136746200-136750200	Weak transcription	Primary B cells from peripheral blood	blood
17	chr9:136746200-136750800	Enhancers	Fetal Brain Male	brain
18	chr9:136746800-136750000	Weak transcription	Ovary	ovary
19	chr9:136747200-136752400	Weak transcription	Colon Smooth Muscle	Colon
20	chr9:136747200-136753600	Weak transcription	Stomach Mucosa	stomach
21	chr9:136747600-136749800	Enhancers	Pancreas	Pancrea
22	chr9:136747600-136750000	Weak transcription	Fetal Heart	heart
23	chr9:136747600-136750400	Weak transcription	Lung	lung
24	chr9:136747600-136750600	Weak transcription	Gastric	stomach
25	chr9:136747600-136752600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr9:136747600-136753200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr9:136747600-136753400	Enhancers	Fetal Muscle Trunk	muscle
28	chr9:136747600-136753600	Weak transcription	NHLF	lung
29	chr9:136747600-136754800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr9:136747600-136780800	Weak transcription	Right Atrium	heart
31	chr9:136747800-136753000	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr9:136747800-136753000	Weak transcription	NH-A	brain
33	chr9:136747800-136753200	Weak transcription	Brain Substantia Nigra	brain
34	chr9:136748200-136751600	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr9:136748200-136751600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr9:136748200-136751800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr9:136748200-136753200	Weak transcription	Brain Anterior Caudate	brain
38	chr9:136748200-136762200	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr9:136748400-136753000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr9:136748400-136753200	Weak transcription	Brain Cingulate Gyrus	brain
41	chr9:136748400-136758000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr9:136748600-136749800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr9:136748600-136750000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr9:136748600-136750000	Weak transcription	Fetal Lung	lung
45	chr9:136748600-136750600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr9:136748600-136751200	Strong transcription	Fetal Intestine Small	intestine
47	chr9:136748600-136751600	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr9:136748600-136751800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr9:136748600-136752200	Strong transcription	Fetal Stomach	stomach
50	chr9:136748600-136753000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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