Variant report

Variant	rs2156323
Chromosome Location	chr9:136720821-136720822
allele	C/T
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:136719836..136721567-chr9:136722658..136724295,2	MCF-7	breast:
2	chr9:136707416..136709082-chr9:136718802..136721246,2	MCF-7	breast:
3	chr9:136713073..136715436-chr9:136719455..136721835,2	K562	blood:
4	chr9:136720347..136721280-chrX:15692525..15693445,2	Hela-S3	cervix:
5	chr9:136720764..136723622-chr9:136736992..136740613,4	MCF-7	breast:
6	chr9:136646541..136648587-chr9:136720513..136723174,2	MCF-7	breast:
7	chr9:136716723..136719526-chr9:136720633..136722987,2	MCF-7	breast:
8	chr9:136708244..136711057-chr9:136719535..136721439,2	MCF-7	breast:
9	chr9:136718031..136721993-chr9:136856767..136859513,3	MCF-7	breast:
10	chr9:136711109..136713982-chr9:136718065..136723456,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000186312	Chromatin interaction
ENSG00000160293	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10821526	0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs10821530	0.85[AMR][1000 genomes]
rs10993820	0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10993822	1.00[ASN][1000 genomes]
rs10993823	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993824	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993826	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10993828	1.00[ASN][1000 genomes]
rs10993829	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10993830	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10993832	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12000549	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12005762	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12341505	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12376343	0.82[AMR][1000 genomes]
rs12377799	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1557679	0.90[ASN][1000 genomes]
rs17663678	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2073928	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2073929	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2073930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2260095	0.87[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2261150	0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs2428123	0.90[ASN][1000 genomes]
rs2428124	1.00[ASN][1000 genomes]
rs2428126	0.90[ASN][1000 genomes]
rs2428129	0.90[ASN][1000 genomes]
rs2486350	0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs2486351	0.93[CEU][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs2502765	0.90[ASN][1000 genomes]
rs2510254	0.93[CEU][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs28436700	0.90[ASN][1000 genomes]
rs35711919	1.00[ASN][1000 genomes]
rs35776936	1.00[ASN][1000 genomes]
rs3780741	1.00[MEX][hapmap];0.82[AMR][1000 genomes]
rs3819500	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3819502	0.93[CEU][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs3819503	0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs3819504	1.00[ASN][1000 genomes]
rs3819505	1.00[ASN][1000 genomes]
rs55646136	1.00[ASN][1000 genomes]
rs55939286	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56745684	0.90[ASN][1000 genomes]
rs56868628	0.88[ASN][1000 genomes]
rs58816065	0.90[ASN][1000 genomes]
rs67484139	1.00[ASN][1000 genomes]
rs7023551	0.80[CHD][hapmap]
rs7025939	0.93[CEU][hapmap]
rs7038256	0.93[CEU][hapmap]
rs72762854	1.00[ASN][1000 genomes]
rs72762864	1.00[ASN][1000 genomes]
rs739466	0.87[CEU][hapmap]
rs7852459	1.00[MEX][hapmap]
rs7853626	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];1.00[ASN][1000 genomes]

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	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
5	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
6	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
7	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
8	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
9	esv3401000	chr9:136717131-136721429	Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2156323	LCN8	cis	parietal	SCAN
rs2156323	BAT2L1	cis	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136675200-136728400	Weak transcription	Esophagus	oesophagus
2	chr9:136705400-136726800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr9:136705800-136721000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr9:136705800-136724400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr9:136705800-136726000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr9:136705800-136729400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr9:136706000-136726400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr9:136707200-136726600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr9:136708000-136721000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr9:136709000-136728600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr9:136710000-136727400	Weak transcription	Brain Substantia Nigra	brain
12	chr9:136710600-136727200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr9:136710800-136725600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr9:136710800-136728600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr9:136711000-136721000	Weak transcription	A549	lung
16	chr9:136711000-136725800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr9:136711400-136737800	Weak transcription	NH-A	brain
18	chr9:136711600-136727400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr9:136712200-136721400	Strong transcription	Fetal Stomach	stomach
20	chr9:136714600-136721200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr9:136714600-136722800	Weak transcription	HMEC	breast
22	chr9:136714600-136729400	Weak transcription	NHEK	skin
23	chr9:136715200-136725600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr9:136715400-136723000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:136716600-136722000	Weak transcription	GM12878-XiMat	blood
26	chr9:136717200-136721200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr9:136717200-136728600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr9:136717600-136722600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr9:136717800-136724600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr9:136718200-136723000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr9:136718200-136726400	Strong transcription	Primary B cells from peripheral blood	blood
32	chr9:136718400-136721000	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr9:136718400-136727400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr9:136718600-136722400	Genic enhancers	Fetal Intestine Small	intestine
35	chr9:136719000-136724000	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr9:136719000-136724400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr9:136719000-136725600	Weak transcription	Gastric	stomach
38	chr9:136719200-136721200	Genic enhancers	Pancreas	Pancrea
39	chr9:136719200-136721400	Enhancers	Fetal Kidney	kidney
40	chr9:136719200-136722200	Weak transcription	Brain Hippocampus Middle	brain
41	chr9:136719400-136723000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr9:136719400-136725600	Weak transcription	Aorta	Aorta
43	chr9:136719400-136728200	Weak transcription	NHDF-Ad	bronchial
44	chr9:136719600-136722400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr9:136719600-136727400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr9:136719600-136727800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr9:136719800-136721000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr9:136719800-136722200	Weak transcription	Brain Germinal Matrix	brain
49	chr9:136719800-136722200	Enhancers	Placenta	Placenta
50	chr9:136720000-136721000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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