Variant report

Variant	rs17728942
Chromosome Location	chr12:8288403-8288404
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFF	chr12:8288111-8288404	HepG2	liver:	n/a	chr12:8288245-8288263
2	SMC3	chr12:8288287-8288426	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ZNF705A	TF binding region
POU5F1P3	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs7294894	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048545	chr12:7778760-8608231	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv541368	chr12:7778760-8608231	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	esv1795892	chr12:7856819-8508693	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	esv2758292	chr12:7856819-8623987	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	esv2759877	chr12:7856819-8623987	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
6	nsv428270	chr12:7856819-8623987	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
7	esv1793572	chr12:7995827-8568422	Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
8	nsv916941	chr12:8003501-8608220	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
9	nsv1040958	chr12:8177050-8309724	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
10	nsv541396	chr12:8177050-8309724	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
11	nsv430460	chr12:8225225-8388656	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv1040302	chr12:8245364-8695612	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
13	nsv541397	chr12:8245364-8695612	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
14	esv1796538	chr12:8276546-8508693	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv427902	chr12:8276546-8623987	Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
16	esv2757488	chr12:8280755-8580804	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17728942	LEPREL2	cis	cerebellum	SCAN
rs17728942	RAD51AP1	cis	cerebellum	SCAN
rs17728942	KLRB1	cis	parietal	SCAN
rs17728942	GNB3	cis	cerebellum	SCAN
rs17728942	C1RL	cis	cerebellum	SCAN
rs17728942	CD9	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:8249600-8293200	Weak transcription	Pancreas	Pancrea
2	chr12:8249600-8298200	Weak transcription	HSMMtube	muscle
3	chr12:8250000-8293600	Weak transcription	Lung	lung
4	chr12:8250000-8298400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:8250200-8298400	Weak transcription	Colon Smooth Muscle	Colon
6	chr12:8251000-8292200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr12:8251000-8293200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr12:8251000-8293800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr12:8251000-8298400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr12:8252200-8292000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr12:8255000-8295200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr12:8255200-8290400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr12:8257400-8289400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr12:8258600-8290400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr12:8260800-8293000	Weak transcription	Psoas Muscle	Psoas
16	chr12:8261800-8290400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr12:8262000-8290400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr12:8269200-8298400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr12:8271200-8298400	Weak transcription	Brain Hippocampus Middle	brain
20	chr12:8271600-8298400	Weak transcription	Aorta	Aorta
21	chr12:8273200-8292000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr12:8273800-8298400	Weak transcription	Fetal Brain Female	brain
23	chr12:8274800-8293200	Weak transcription	Spleen	Spleen
24	chr12:8276400-8289400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:8277000-8289800	Weak transcription	Fetal Intestine Small	intestine
26	chr12:8277000-8295000	Weak transcription	Left Ventricle	heart
27	chr12:8278400-8296600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr12:8280000-8288800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr12:8280000-8290400	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr12:8280600-8290400	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr12:8280600-8292000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr12:8280800-8292600	Weak transcription	Fetal Thymus	thymus
33	chr12:8280800-8292600	Weak transcription	Thymus	Thymus
34	chr12:8280800-8293000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr12:8280800-8293200	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr12:8281200-8298200	Weak transcription	Fetal Stomach	stomach
37	chr12:8281400-8293400	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr12:8281400-8295200	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr12:8282400-8295000	Weak transcription	Right Ventricle	heart
40	chr12:8282600-8294400	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr12:8283400-8290600	Weak transcription	Fetal Muscle Leg	muscle
42	chr12:8283600-8298400	Weak transcription	Fetal Lung	lung
43	chr12:8284400-8289600	Weak transcription	Primary B cells from peripheral blood	blood
44	chr12:8285800-8290800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr12:8286600-8290600	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr12:8286600-8298800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr12:8286800-8294200	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr12:8287200-8298200	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr12:8287200-8298200	Weak transcription	Brain Substantia Nigra	brain
50	chr12:8287400-8292800	Weak transcription	Fetal Intestine Large	intestine

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