Variant report

Variant	rs3858103
Chromosome Location	chr9:136686389-136686390
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:136685055..136687133-chr9:136857596..136859657,2	MCF-7	breast:
2	chr9:136686248..136688046-chr9:136689663..136693225,3	K562	blood:
3	chr9:136685827..136689292-chr9:136739053..136741402,3	MCF-7	breast:
4	chr9:136681875..136684320-chr9:136685612..136688536,2	K562	blood:

Variant related genes	Relation type
ENSG00000160293	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10123394	1.00[CHB][hapmap]
rs10993810	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10993811	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993812	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993814	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993815	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1179486	1.00[CHB][hapmap]
rs12337948	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12338059	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17663527	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs2428092	1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs2486337	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs2486338	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2486339	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488551	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2488556	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488557	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2502749	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2502750	0.82[EUR][1000 genomes]
rs2502751	0.82[EUR][1000 genomes]
rs2502752	0.90[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28435685	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28491392	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28493540	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28647613	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3858100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3858101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3858102	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4059239	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55776501	0.86[EUR][1000 genomes]
rs62576521	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576522	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576523	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479624	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479625	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029322	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7034680	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7037626	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7038003	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7042529	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7046253	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7848976	1.00[CHB][hapmap]
rs9409864	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv428546	chr9:136541745-136720872	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	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
4	nsv894117	chr9:136600201-136716399	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	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
6	nsv894121	chr9:136629399-136692787	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136643200-136689800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr9:136650600-136688800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr9:136651400-136686400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:136651400-136689000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:136657800-136690600	Weak transcription	Fetal Kidney	kidney
6	chr9:136658600-136691400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr9:136658800-136705400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr9:136659000-136689400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr9:136659000-136702200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr9:136659800-136687000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr9:136661400-136693800	Weak transcription	HMEC	breast
12	chr9:136666600-136686800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:136667800-136690600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr9:136669000-136691200	Weak transcription	NH-A	brain
15	chr9:136669800-136689800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr9:136670000-136692600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr9:136673000-136686600	Weak transcription	HSMMtube	muscle
18	chr9:136673200-136705000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr9:136673800-136687000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr9:136674600-136699000	Weak transcription	Aorta	Aorta
21	chr9:136674800-136688200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr9:136675000-136688600	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr9:136675200-136728400	Weak transcription	Esophagus	oesophagus
24	chr9:136675400-136691600	Weak transcription	Lung	lung
25	chr9:136675400-136703200	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr9:136675400-136709400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr9:136675600-136698000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr9:136675600-136704800	Weak transcription	Adipose Nuclei	Adipose
29	chr9:136676000-136688800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr9:136676000-136699800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr9:136677000-136705000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr9:136678800-136688000	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr9:136679000-136686600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr9:136679200-136696800	Weak transcription	Gastric	stomach
35	chr9:136679800-136691600	Weak transcription	Brain Hippocampus Middle	brain
36	chr9:136680000-136696800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr9:136680200-136686800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr9:136680200-136691200	Weak transcription	Fetal Brain Female	brain
39	chr9:136680200-136691400	Weak transcription	Right Ventricle	heart
40	chr9:136680200-136691800	Weak transcription	Right Atrium	heart
41	chr9:136680200-136693600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr9:136680200-136693800	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr9:136680400-136686800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr9:136680400-136690400	Weak transcription	Brain Germinal Matrix	brain
45	chr9:136681400-136687200	Weak transcription	Fetal Brain Male	brain
46	chr9:136681400-136690800	Weak transcription	Fetal Lung	lung
47	chr9:136682200-136692400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr9:136682200-136701000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr9:136683200-136688000	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr9:136683800-136691000	Weak transcription	HSMM	muscle

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