Variant report

Variant	rs1196758
Chromosome Location	chr12:105604147-105604148
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:105586360..105589934-chr12:105601343..105605180,3	MCF-7	breast:
2	chr12:105602998..105604968-chr12:105605214..105607629,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136044	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10861327	0.81[CEU][hapmap]
rs10861328	0.81[CEU][hapmap]
rs10861329	0.82[CEU][hapmap]
rs10861330	0.82[CEU][hapmap]
rs10861335	0.82[CEU][hapmap]
rs10861336	0.82[CEU][hapmap]
rs1107756	0.95[CHB][hapmap];0.80[ASN][1000 genomes]
rs11112347	0.81[CEU][hapmap]
rs11112350	0.82[CEU][hapmap]
rs11112351	0.82[CEU][hapmap]
rs11112416	0.90[CHB][hapmap]
rs11612252	0.82[CEU][hapmap]
rs11613261	0.81[CEU][hapmap]
rs1196750	0.82[EUR][1000 genomes]
rs1196751	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1196752	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196761	0.85[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1196766	0.96[CEU][hapmap];0.83[YRI][hapmap];0.80[EUR][1000 genomes]
rs1196767	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs1196768	0.95[CEU][hapmap]
rs1196769	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs1196771	0.80[ASN][1000 genomes]
rs1196781	0.96[CEU][hapmap]
rs1196788	0.96[CEU][hapmap]
rs1196794	0.80[ASN][1000 genomes]
rs1196796	0.96[CEU][hapmap]
rs1196804	0.96[CEU][hapmap]
rs1196814	0.96[CEU][hapmap];0.81[YRI][hapmap]
rs1196836	0.96[CEU][hapmap]
rs1196838	0.93[CEU][hapmap]
rs1196845	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1196854	0.81[EUR][1000 genomes]
rs1196856	0.81[EUR][1000 genomes]
rs1196865	0.81[YRI][hapmap]
rs1196866	0.81[EUR][1000 genomes]
rs1196868	0.81[EUR][1000 genomes]
rs1196878	0.92[CEU][hapmap];0.85[YRI][hapmap]
rs1196882	0.85[CEU][hapmap]
rs1201657	0.96[CEU][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1211627	0.81[ASN][1000 genomes]
rs12581638	0.81[CEU][hapmap]
rs12815031	0.90[CHB][hapmap];0.80[JPT][hapmap]
rs1317955	0.90[CHB][hapmap]
rs1732378	0.85[CEU][hapmap];0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1732379	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2246510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2264066	0.96[CEU][hapmap];0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2293644	0.90[CHB][hapmap]
rs2374448	0.96[CEU][hapmap]
rs2440695	0.95[CHB][hapmap];0.80[ASN][1000 genomes]
rs2440708	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs2440717	0.96[CEU][hapmap]
rs2464184	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs4144468	0.82[CEU][hapmap]
rs727888	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs7308195	0.81[CEU][hapmap]
rs7310488	0.96[CEU][hapmap]
rs750060	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs752471	0.85[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs880797	0.95[CHB][hapmap]
rs881279	0.90[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832506	chr12:105461274-105637561	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv455704	chr12:105583877-105651356	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
3	nsv560053	chr12:105583877-105651356	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1196758	ALDH1L2	Cis_1M	lymphoblastoid	RTeQTL
rs1196758	APPL2	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105546800-105625200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:105558800-105615200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:105571400-105617800	Weak transcription	K562	blood
4	chr12:105576400-105606000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:105577000-105607200	Strong transcription	Sigmoid Colon	Sigmoid Colon
6	chr12:105577400-105616200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:105577800-105605400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr12:105577800-105605600	Strong transcription	Primary B cells from cord blood	blood
9	chr12:105577800-105607400	Strong transcription	Duodenum Mucosa	Duodenum
10	chr12:105578000-105607400	Strong transcription	Fetal Brain Female	brain
11	chr12:105578000-105623200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr12:105578200-105620000	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr12:105579000-105605200	Strong transcription	Fetal Muscle Leg	muscle
14	chr12:105579000-105612400	Strong transcription	Stomach Smooth Muscle	stomach
15	chr12:105580200-105613200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:105581200-105605400	Strong transcription	Fetal Muscle Trunk	muscle
17	chr12:105581800-105605200	Strong transcription	Brain Germinal Matrix	brain
18	chr12:105583600-105605600	Strong transcription	Right Ventricle	heart
19	chr12:105584000-105627000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr12:105587400-105609000	Weak transcription	Fetal Brain Male	brain
21	chr12:105589200-105612200	Weak transcription	Psoas Muscle	Psoas
22	chr12:105589400-105608600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr12:105589400-105612400	Weak transcription	Fetal Heart	heart
24	chr12:105590200-105620000	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr12:105590400-105618800	Strong transcription	Primary B cells from peripheral blood	blood
26	chr12:105591000-105619400	Strong transcription	Primary T cells from cord blood	blood
27	chr12:105594000-105605400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr12:105594200-105604400	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr12:105594400-105614400	Weak transcription	Small Intestine	intestine
30	chr12:105594600-105607200	Strong transcription	Fetal Intestine Large	intestine
31	chr12:105594600-105607600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr12:105595000-105612800	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr12:105595000-105618800	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr12:105595200-105607800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr12:105595600-105612800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr12:105595800-105605800	Strong transcription	Adipose Nuclei	Adipose
37	chr12:105595800-105612000	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr12:105595800-105612200	Weak transcription	Right Atrium	heart
39	chr12:105595800-105616600	Strong transcription	Primary hematopoietic stem cells	blood
40	chr12:105596000-105617000	Strong transcription	Fetal Lung	lung
41	chr12:105596200-105605400	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr12:105596400-105621800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr12:105596600-105607600	Strong transcription	Liver	Liver
44	chr12:105597200-105607800	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr12:105599400-105612400	Strong transcription	Brain Anterior Caudate	brain
46	chr12:105599600-105604800	Strong transcription	HSMM	muscle
47	chr12:105599600-105605600	Strong transcription	Brain Substantia Nigra	brain
48	chr12:105599600-105605600	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr12:105599600-105605600	Strong transcription	NHLF	lung
50	chr12:105599600-105606200	Strong transcription	NH-A	brain

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