Variant report

Variant	rs7974437
Chromosome Location	chr12:31735697-31735698
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:31733749..31740034-chr12:31741014..31744449,13	K562	blood:
2	chr12:31735394..31738773-chr12:31741793..31744223,3	MCF-7	breast:
3	chr12:31730582..31735738-chr12:31737602..31740641,5	K562	blood:
4	chr12:31733774..31735738-chr12:31738884..31740641,2	K562	blood:
5	chr12:31733856..31736824-chr12:31741317..31742941,2	K562	blood:

Variant related genes	Relation type
ENSG00000170456	Chromatin interaction
ENSG00000255867	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1012154	0.87[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap]
rs10743757	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10743758	0.94[CHB][hapmap];0.96[CHD][hapmap];0.82[JPT][hapmap]
rs10743759	0.92[ASN][1000 genomes]
rs10771832	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10771838	0.85[ASN][1000 genomes]
rs10771843	0.92[ASN][1000 genomes]
rs10771844	0.83[ASN][1000 genomes]
rs10771845	0.89[ASN][1000 genomes]
rs10771846	0.94[ASN][1000 genomes]
rs10843942	0.83[ASN][1000 genomes]
rs10843947	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs10843958	0.87[ASN][1000 genomes]
rs10843959	0.87[ASN][1000 genomes]
rs10843963	0.92[ASN][1000 genomes]
rs11051418	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs11051435	0.85[ASN][1000 genomes]
rs11051437	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[ASN][1000 genomes]
rs11051439	0.85[ASN][1000 genomes]
rs11051441	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11051456	0.89[AFR][1000 genomes]
rs1150953	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs1150955	0.81[CHB][hapmap]
rs11615961	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs1259235	0.87[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap]
rs1259236	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1259355	0.85[ASN][1000 genomes]
rs1259356	0.81[CHB][hapmap]
rs1259359	0.81[CHB][hapmap]
rs1259401	0.82[EUR][1000 genomes]
rs1259422	0.83[EUR][1000 genomes]
rs1259428	1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs1259432	1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs1259437	0.81[CHB][hapmap]
rs1271128	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1271663	0.83[EUR][1000 genomes]
rs1272773	0.81[CHB][hapmap]
rs1469673	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1677154	0.83[EUR][1000 genomes]
rs1677189	0.80[CHB][hapmap]
rs1716216	0.87[CHB][hapmap];0.85[TSI][hapmap]
rs1996693	0.92[ASN][1000 genomes]
rs2116704	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2352048	0.94[ASN][1000 genomes]
rs2374190	0.88[ASW][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap]
rs2568884	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs2617190	0.82[JPT][hapmap]
rs2617191	0.81[CHB][hapmap]
rs2617200	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs2682697	0.88[JPT][hapmap]
rs3803113	0.99[ASN][1000 genomes]
rs3844573	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs3850965	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3898368	0.94[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4482118	0.94[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4930980	0.92[ASN][1000 genomes]
rs4931501	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4931506	0.86[ASN][1000 genomes]
rs4931507	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6416254	0.83[ASN][1000 genomes]
rs6487992	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs708209	0.93[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap]
rs7133082	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7135856	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[ASN][1000 genomes]
rs7136476	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs7136943	0.87[ASN][1000 genomes]
rs7137406	0.87[ASN][1000 genomes]
rs7294574	0.88[ASW][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs7302698	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7307593	0.92[ASN][1000 genomes]
rs7307616	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7313118	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7313689	0.86[ASN][1000 genomes]
rs7314417	0.86[ASN][1000 genomes]
rs793174	0.81[CHB][hapmap]
rs793176	0.86[CHB][hapmap]
rs793177	0.81[CHB][hapmap]
rs793186	0.81[CHB][hapmap]
rs7954023	0.87[ASN][1000 genomes]
rs7954595	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7959877	0.94[ASW][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7962896	0.94[ASW][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7963161	0.84[ASN][1000 genomes]
rs7967832	0.84[ASN][1000 genomes]
rs7968291	0.81[ASN][1000 genomes]
rs7975761	0.88[ASW][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs7976644	0.94[ASW][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7977453	0.87[ASN][1000 genomes]
rs899159	0.81[CHB][hapmap]
rs9738834	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv1836923	chr12:31539122-31761172	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv898965	chr12:31631819-31771689	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv832365	chr12:31642811-31808532	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv1842653	chr12:31670378-31744033	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	esv1797962	chr12:31733044-31761172	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7974437	PTHLH	cis	cerebellum	SCAN
rs7974437	DENND5B	cis	parietal	SCAN
rs7974437	FLJ13224	cis	cerebellum	SCAN
rs7974437	DENND5B	cis	cerebellum	SCAN
rs7974437	KCNAB2	trans	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31721600-31742400	Weak transcription	Aorta	Aorta
2	chr12:31726400-31742000	Weak transcription	Fetal Intestine Large	intestine
3	chr12:31726600-31738000	Weak transcription	Liver	Liver
4	chr12:31727000-31738000	Weak transcription	Small Intestine	intestine
5	chr12:31727800-31737200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:31728000-31741000	Weak transcription	Right Ventricle	heart
7	chr12:31728200-31738000	Weak transcription	Hela-S3	cervix
8	chr12:31728400-31741800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:31728800-31738200	Weak transcription	Fetal Intestine Small	intestine
10	chr12:31728800-31738200	Weak transcription	HepG2	liver
11	chr12:31729800-31737400	Weak transcription	Left Ventricle	heart
12	chr12:31730800-31738200	Weak transcription	Primary B cells from cord blood	blood
13	chr12:31731200-31736800	Weak transcription	GM12878-XiMat	blood
14	chr12:31731800-31736600	Weak transcription	HUVEC	blood vessel
15	chr12:31731800-31737000	Weak transcription	Brain Germinal Matrix	brain
16	chr12:31732000-31737000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr12:31732000-31737200	Weak transcription	Brain Anterior Caudate	brain
18	chr12:31732000-31737200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr12:31732000-31737400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr12:31732000-31738000	Weak transcription	NHLF	lung
21	chr12:31732000-31741400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr12:31732200-31737200	Weak transcription	Brain Hippocampus Middle	brain
23	chr12:31732200-31737800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr12:31732200-31738200	Weak transcription	Brain Angular Gyrus	brain
25	chr12:31732200-31738200	Weak transcription	Colon Smooth Muscle	Colon
26	chr12:31732200-31738200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr12:31732200-31741600	Weak transcription	Fetal Kidney	kidney
28	chr12:31732400-31736600	Weak transcription	Primary B cells from peripheral blood	blood
29	chr12:31732400-31737400	Weak transcription	Psoas Muscle	Psoas
30	chr12:31732400-31738000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr12:31732400-31738200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr12:31732400-31741000	Weak transcription	Pancreas	Pancrea
33	chr12:31732600-31737000	Weak transcription	Fetal Muscle Leg	muscle
34	chr12:31732600-31737800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr12:31734000-31737000	Weak transcription	Ovary	ovary
36	chr12:31734600-31735800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:31734800-31735800	Enhancers	HSMM	muscle
38	chr12:31734800-31735800	Enhancers	NHEK	skin
39	chr12:31734800-31736000	Enhancers	Osteobl	bone
40	chr12:31735000-31735800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:31735000-31735800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr12:31735000-31736200	Enhancers	A549	lung
43	chr12:31735000-31737400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr12:31735000-31738200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr12:31735200-31735800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr12:31735400-31737000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr12:31735400-31737000	Weak transcription	HSMMtube	muscle
48	chr12:31735400-31737800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr12:31735400-31738000	Weak transcription	NH-A	brain
50	chr12:31735400-31738200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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