Variant report

Variant	rs10783387
Chromosome Location	chr12:51180143-51180144
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:51177098..51179520-chr12:51179532..51182751,3	K562	blood:
2	chr12:51156412..51159922-chr12:51179248..51181916,4	MCF-7	breast:
3	chr12:51168355..51171180-chr12:51178440..51181054,2	K562	blood:
4	chr12:51175977..51178519-chr12:51179089..51181352,2	MCF-7	breast:
5	chr12:51179438..51182295-chr12:51203599..51205649,2	MCF-7	breast:
6	chr12:51155325..51162343-chr12:51172009..51182370,14	MCF-7	breast:
7	chr12:51160285..51163042-chr12:51178907..51180859,2	MCF-7	breast:
8	chr12:51167462..51169093-chr12:51179939..51182142,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000123268	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10783386	0.82[EUR][1000 genomes]
rs10876084	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10876087	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876092	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876098	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11169506	0.94[CHB][hapmap];0.93[JPT][hapmap];0.81[YRI][hapmap]
rs11169523	0.83[CHB][hapmap];0.81[YRI][hapmap]
rs11169524	0.81[ASW][hapmap];0.95[CHB][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap]
rs11169562	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169563	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11169567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169570	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11169571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11169572	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11169578	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1129406	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11503907	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12372718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12427378	0.83[CHB][hapmap];0.92[GIH][hapmap];0.93[TSI][hapmap]
rs12818741	0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap]
rs1316607	0.81[ASW][hapmap];0.83[CHB][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap]
rs13378012	0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap]
rs2090852	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs2139930	0.95[CHB][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap]
rs2280503	0.81[ASW][hapmap];0.95[CHB][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap];0.81[ASN][1000 genomes]
rs34645899	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34863430	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35353300	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3742062	0.95[CHB][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap]
rs4307773	0.92[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs4388959	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs4768903	0.82[TSI][hapmap]
rs4986838	0.94[CHB][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61926299	0.82[EUR][1000 genomes]
rs61926301	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61926303	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7133974	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7137845	0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap]
rs7297504	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7298665	0.82[YRI][hapmap]
rs7304335	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7306677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7974517	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs864899	0.92[CEU][hapmap]
rs876080	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs9943712	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3497481	chr12:51150734-51185125	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
2	esv3497482	chr12:51151798-51185232	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
3	esv3386327	chr12:51154734-51184232	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
4	nsv899077	chr12:51160612-51188397	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10783387	LASS5	cis	cerebellum	SCAN
rs10783387	LASS5	cis	parietal	SCAN
rs10783387	KRT73	cis	parietal	SCAN
rs10783387	ATF1	cis	Adipose Subcutaneous	GTEx
rs10783387	DIP2B	Cis_1M	lymphoblastoid	RTeQTL
rs10783387	DIP2B	cis	cerebellum	SCAN
rs10783387	ATF1	cis	Artery Tibial	GTEx
rs10783387	FAIM2	cis	cerebellum	SCAN
rs10783387	ATF1	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51159000-51180200	Weak transcription	Esophagus	oesophagus
2	chr12:51159200-51192600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:51159400-51192600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:51159600-51189200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr12:51159800-51180600	Weak transcription	Fetal Lung	lung
6	chr12:51159800-51189600	Weak transcription	Spleen	Spleen
7	chr12:51159800-51190400	Weak transcription	Fetal Kidney	kidney
8	chr12:51159800-51191200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr12:51160000-51189800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr12:51160000-51190800	Weak transcription	Right Ventricle	heart
11	chr12:51160200-51180200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr12:51160200-51189600	Weak transcription	Pancreas	Pancrea
13	chr12:51160200-51189800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr12:51160800-51189600	Weak transcription	Brain Angular Gyrus	brain
15	chr12:51160800-51190600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr12:51161000-51189800	Weak transcription	Ovary	ovary
17	chr12:51161800-51180400	Weak transcription	Colonic Mucosa	Colon
18	chr12:51164400-51189600	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr12:51167000-51180400	Weak transcription	Fetal Brain Female	brain
20	chr12:51172600-51190600	Weak transcription	Fetal Brain Male	brain
21	chr12:51173000-51189600	Weak transcription	Colon Smooth Muscle	Colon
22	chr12:51173200-51190000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr12:51173600-51180200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr12:51174000-51180400	Strong transcription	Fetal Intestine Small	intestine
25	chr12:51174000-51181600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:51175000-51180200	Weak transcription	Lung	lung
27	chr12:51175000-51180400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr12:51175000-51180600	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr12:51175400-51192200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr12:51176000-51180200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr12:51176000-51180400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr12:51176000-51180600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:51176000-51180800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr12:51176000-51182600	Weak transcription	Brain Anterior Caudate	brain
35	chr12:51176000-51184400	Weak transcription	K562	blood
36	chr12:51176000-51189000	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr12:51176000-51189400	Weak transcription	Adipose Nuclei	Adipose
38	chr12:51176000-51189400	Weak transcription	Brain Hippocampus Middle	brain
39	chr12:51176200-51189600	Weak transcription	Duodenum Mucosa	Duodenum
40	chr12:51176800-51189000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr12:51177200-51180400	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr12:51177400-51189200	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr12:51177800-51180400	Strong transcription	Dnd41	blood
44	chr12:51178000-51182200	Strong transcription	Primary B cells from cord blood	blood
45	chr12:51178200-51180200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr12:51178200-51180800	Enhancers	Psoas Muscle	Psoas
47	chr12:51178200-51181000	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr12:51178200-51182000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr12:51178200-51184200	Enhancers	Placenta	Placenta
50	chr12:51178400-51181400	Weak transcription	Primary T cells fromperipheralblood	blood

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