Variant report

Variant	rs1561422
Chromosome Location	chr12:51188397-51188398
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:51156472..51159680-chr12:51184419..51189273,5	MCF-7	breast:
2	chr12:51156696..51159478-chr12:51186693..51190528,4	K562	blood:

Variant related genes	Relation type
ENSG00000123268	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10506296	0.84[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs10735827	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10747590	0.89[ASN][1000 genomes]
rs10747592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10747593	0.93[ASN][1000 genomes]
rs10783388	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783390	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs10876082	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10876083	0.98[ASN][1000 genomes]
rs10876085	0.98[ASN][1000 genomes]
rs10876088	0.99[ASN][1000 genomes]
rs10876091	0.97[ASN][1000 genomes]
rs1109726	0.82[EUR][1000 genomes]
rs11169551	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11169553	0.98[ASN][1000 genomes]
rs11169556	0.99[ASN][1000 genomes]
rs11609941	0.82[EUR][1000 genomes]
rs1521515	0.84[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1521517	0.84[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap]
rs17124907	0.84[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1815010	0.87[ASN][1000 genomes]
rs2246840	0.84[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2252595	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs2554862	0.95[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs2684886	0.84[ASN][1000 genomes]
rs2684890	0.84[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2684891	0.84[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2684906	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs2700486	0.85[ASN][1000 genomes]
rs3803181	0.84[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs3825401	0.84[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs4143663	0.84[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs4768862	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4768909	0.85[ASN][1000 genomes]
rs4768915	0.80[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4768920	0.99[ASN][1000 genomes]
rs56818625	0.81[ASN][1000 genomes]
rs57328764	0.87[ASN][1000 genomes]
rs57602501	0.82[EUR][1000 genomes]
rs57729468	0.85[EUR][1000 genomes]
rs58301497	0.85[ASN][1000 genomes]
rs59284993	0.92[ASN][1000 genomes]
rs61926300	0.88[ASN][1000 genomes]
rs6580766	0.99[ASN][1000 genomes]
rs6580767	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6580768	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6580769	0.89[EUR][1000 genomes]
rs6580770	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs66838741	0.89[EUR][1000 genomes]
rs66947035	0.88[EUR][1000 genomes]
rs67218241	0.84[EUR][1000 genomes]
rs67356137	0.88[EUR][1000 genomes]
rs67934435	0.83[EUR][1000 genomes]
rs7132443	0.81[ASN][1000 genomes]
rs7303202	0.87[ASN][1000 genomes]
rs7304793	0.96[ASN][1000 genomes]
rs7307788	0.86[EUR][1000 genomes]
rs7308872	0.86[ASN][1000 genomes]
rs7487150	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7958114	0.88[EUR][1000 genomes]
rs7959129	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7960015	0.82[EUR][1000 genomes]
rs7964642	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7969251	0.81[ASN][1000 genomes]
rs7976942	0.89[EUR][1000 genomes]
rs7977064	0.88[EUR][1000 genomes]
rs7978559	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs7979165	0.91[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs7979474	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs829112	0.95[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs829114	0.88[EUR][1000 genomes]
rs829115	0.88[EUR][1000 genomes]
rs829125	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs829133	0.83[JPT][hapmap]
rs865489	0.88[EUR][1000 genomes]
rs865490	0.96[ASN][1000 genomes]
rs939631	0.84[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs951591	0.84[CHB][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1561422	LASS5	cis	parietal	SCAN
rs1561422	DIP2B	cis	cerebellum	SCAN
rs1561422	ATF1	cis	cerebellum	SCAN
rs1561422	AMIGO2	cis	cerebellum	SCAN
rs1561422	DHH	cis	parietal	SCAN
rs1561422	MCRS1	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51159200-51192600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:51159400-51192600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr12:51159600-51189200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr12:51159800-51189600	Weak transcription	Spleen	Spleen
5	chr12:51159800-51190400	Weak transcription	Fetal Kidney	kidney
6	chr12:51159800-51191200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr12:51160000-51189800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr12:51160000-51190800	Weak transcription	Right Ventricle	heart
9	chr12:51160200-51189600	Weak transcription	Pancreas	Pancrea
10	chr12:51160200-51189800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr12:51160800-51189600	Weak transcription	Brain Angular Gyrus	brain
12	chr12:51160800-51190600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr12:51161000-51189800	Weak transcription	Ovary	ovary
14	chr12:51164400-51189600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr12:51172600-51190600	Weak transcription	Fetal Brain Male	brain
16	chr12:51173000-51189600	Weak transcription	Colon Smooth Muscle	Colon
17	chr12:51173200-51190000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr12:51175400-51192200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr12:51176000-51189000	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr12:51176000-51189400	Weak transcription	Adipose Nuclei	Adipose
21	chr12:51176000-51189400	Weak transcription	Brain Hippocampus Middle	brain
22	chr12:51176200-51189600	Weak transcription	Duodenum Mucosa	Duodenum
23	chr12:51176800-51189000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr12:51177400-51189200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr12:51178400-51192400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr12:51178600-51189000	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr12:51178600-51189800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr12:51178800-51192600	Weak transcription	Fetal Heart	heart
29	chr12:51179600-51189400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr12:51179800-51189200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr12:51179800-51189600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr12:51180000-51189600	Weak transcription	Left Ventricle	heart
33	chr12:51180000-51189600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr12:51180200-51189600	Weak transcription	Small Intestine	intestine
35	chr12:51180600-51188800	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr12:51180600-51192800	Weak transcription	Esophagus	oesophagus
37	chr12:51180800-51189600	Weak transcription	Lung	lung
38	chr12:51180800-51189600	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr12:51180800-51189800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr12:51180800-51189800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr12:51180800-51189800	Weak transcription	Gastric	stomach
42	chr12:51180800-51189800	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr12:51180800-51190400	Weak transcription	Psoas Muscle	Psoas
44	chr12:51180800-51190800	Weak transcription	Colonic Mucosa	Colon
45	chr12:51180800-51191800	Weak transcription	Aorta	Aorta
46	chr12:51180800-51204400	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr12:51181000-51189000	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr12:51181000-51189400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr12:51181000-51189600	Weak transcription	Liver	Liver
50	chr12:51181000-51189800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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