Variant report

Variant	rs703681
Chromosome Location	chr12:105143135-105143136
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	chr12:105130507..105133001-chr12:105142038..105144910,2	MCF-7	breast:
2	chr12:105141843..105143930-chr12:105147276..105148926,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1002803	0.94[CEU][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10507184	0.89[CEU][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap]
rs1070316	0.94[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10778358	0.85[CHD][hapmap]
rs1155994	0.89[CEU][hapmap]
rs1316594	0.80[EUR][1000 genomes]
rs1389609	0.84[EUR][1000 genomes]
rs1389612	0.89[CEU][hapmap];0.93[JPT][hapmap]
rs1474459	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs1565813	0.83[CEU][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap]
rs1565815	0.81[EUR][1000 genomes]
rs2131806	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs2141248	0.83[EUR][1000 genomes]
rs2245927	0.80[EUR][1000 genomes]
rs2245931	0.80[EUR][1000 genomes]
rs2248012	0.89[CEU][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes]
rs2249454	0.85[CHD][hapmap]
rs2453154	0.94[CEU][hapmap]
rs2453155	0.94[CEU][hapmap];0.83[GIH][hapmap]
rs2453156	0.94[CEU][hapmap];0.92[JPT][hapmap];0.86[EUR][1000 genomes]
rs2453157	0.85[EUR][1000 genomes]
rs2453160	0.80[EUR][1000 genomes]
rs2453161	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2453166	0.89[CEU][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes]
rs2453167	0.80[EUR][1000 genomes]
rs2453168	0.84[EUR][1000 genomes]
rs2463016	0.80[EUR][1000 genomes]
rs2463017	0.80[EUR][1000 genomes]
rs2463018	0.89[CEU][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.92[EUR][1000 genomes]
rs2463019	0.89[CEU][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs2463025	0.80[EUR][1000 genomes]
rs2463429	0.84[EUR][1000 genomes]
rs2463433	0.80[EUR][1000 genomes]
rs2463437	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs2463438	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs2463439	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2463440	0.94[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2463441	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2463442	0.94[CEU][hapmap];0.87[GIH][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs2463443	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs2463444	0.94[CEU][hapmap];0.93[EUR][1000 genomes]
rs2468083	0.84[EUR][1000 genomes]
rs2468089	0.89[CEU][hapmap]
rs2468092	0.93[JPT][hapmap]
rs2468099	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs2468100	0.81[EUR][1000 genomes]
rs2468105	0.89[CEU][hapmap];0.92[JPT][hapmap]
rs2468109	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2468110	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs2565167	0.80[EUR][1000 genomes]
rs2642110	0.84[EUR][1000 genomes]
rs2642116	0.80[EUR][1000 genomes]
rs2730291	0.94[CEU][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.82[TSI][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4393404	0.88[CHD][hapmap]
rs6539170	0.89[CEU][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap]
rs7135015	0.88[CHD][hapmap]
rs7847	0.91[EUR][1000 genomes]
rs903247	0.94[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs703681	CHST11	Cis_1M	lymphoblastoid	RTeQTL
rs703681	HCFC2	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105130000-105150800	Weak transcription	A549	lung
2	chr12:105130200-105150200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr12:105133800-105151200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:105135600-105143800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr12:105136600-105144800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr12:105136600-105150600	Weak transcription	Gastric	stomach
7	chr12:105136800-105154400	Weak transcription	Right Ventricle	heart
8	chr12:105137000-105143400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr12:105137000-105150800	Weak transcription	Aorta	Aorta
10	chr12:105137000-105152600	Weak transcription	Brain Angular Gyrus	brain
11	chr12:105137200-105144800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr12:105137200-105150600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:105137200-105150600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr12:105137200-105154000	Weak transcription	Brain Substantia Nigra	brain
15	chr12:105137200-105157000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr12:105139000-105144800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:105139000-105147000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr12:105139600-105147200	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr12:105139800-105144200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr12:105139800-105144400	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr12:105139800-105144600	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr12:105139800-105146000	Enhancers	Fetal Thymus	thymus
23	chr12:105140000-105144000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr12:105140000-105144000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr12:105140000-105144200	Enhancers	Primary T cells fromperipheralblood	blood
26	chr12:105140000-105145200	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr12:105140200-105143800	Enhancers	Fetal Muscle Leg	muscle
28	chr12:105140200-105145000	Enhancers	Placenta	Placenta
29	chr12:105140200-105146600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr12:105140400-105143400	Weak transcription	Primary hematopoietic stem cells	blood
31	chr12:105140400-105144000	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr12:105140800-105143400	Enhancers	Primary T cells from cord blood	blood
33	chr12:105141000-105143200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr12:105141000-105144200	Enhancers	H9 Cell Line	embryonic stem cell
35	chr12:105141000-105145800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr12:105141000-105146200	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr12:105141200-105143600	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr12:105141200-105143600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr12:105141200-105145800	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr12:105141400-105143200	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr12:105141400-105143400	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr12:105141400-105143600	Enhancers	Fetal Heart	heart
43	chr12:105141600-105143600	Enhancers	Colon Smooth Muscle	Colon
44	chr12:105141600-105145000	Enhancers	Dnd41	blood
45	chr12:105141600-105155400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr12:105141800-105144200	Enhancers	NHEK	skin
47	chr12:105142000-105143200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr12:105142000-105144200	Enhancers	NHDF-Ad	bronchial
49	chr12:105142000-105144400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr12:105142200-105143400	Enhancers	Primary neutrophils fromperipheralblood	blood

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