Variant report

Variant	rs7973993
Chromosome Location	chr12:104872372-104872373
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104849668..104855401-chr12:104869919..104879346,13	K562	blood:
2	chr12:104869578..104872458-chr12:104877687..104880614,4	K562	blood:
3	chr12:104871756..104873492-chr12:104876935..104879923,2	K562	blood:
4	chr12:104866750..104869514-chr12:104871657..104874435,3	K562	blood:

Variant related genes	Relation type
ENSG00000171310	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10861220	1.00[JPT][hapmap]
rs10861221	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10861222	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10861223	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10861224	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11112069	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs11112070	0.91[ASN][1000 genomes]
rs11112074	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12315283	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1922262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1922263	0.91[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4964809	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66839509	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7299352	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs7313791	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832502	chr12:104833729-104908288	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv832504	chr12:104853331-105028245	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv868	chr12:104858964-104895572	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1042647	chr12:104861494-104888494	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7973993	PMCH	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104855400-104874400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr12:104855400-104874800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:104857000-104873600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:104857800-104873600	Weak transcription	A549	lung
5	chr12:104859200-104879800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr12:104863400-104879200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:104865600-104874600	Weak transcription	HMEC	breast
8	chr12:104866600-104882400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr12:104867400-104874400	Weak transcription	Brain Germinal Matrix	brain
10	chr12:104867400-104874400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr12:104867600-104872400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr12:104867600-104874400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr12:104867600-104876200	Weak transcription	Colonic Mucosa	Colon
14	chr12:104867600-104879400	Weak transcription	Brain Anterior Caudate	brain
15	chr12:104867600-104879600	Weak transcription	Fetal Brain Female	brain
16	chr12:104869200-104872400	Weak transcription	Stomach Mucosa	stomach
17	chr12:104869200-104872600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr12:104869200-104874400	Weak transcription	Fetal Stomach	stomach
19	chr12:104869200-104879400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr12:104869200-104899600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr12:104869400-104874400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr12:104870600-104879200	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr12:104871000-104872400	Flanking Active TSS	Dnd41	blood
24	chr12:104871000-104873200	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:104871000-104873600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr12:104871000-104879200	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr12:104871400-104872600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr12:104871400-104872600	Active TSS	Rectal Mucosa Donor 29	rectum
29	chr12:104871400-104873000	Flanking Active TSS	Primary B cells from cord blood	blood
30	chr12:104871400-104873000	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr12:104871400-104873200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr12:104871400-104873400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr12:104871400-104874800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:104871400-104876400	Weak transcription	Brain Hippocampus Middle	brain
35	chr12:104871600-104872400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr12:104871600-104872400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
37	chr12:104871600-104872600	Flanking Active TSS	Primary hematopoietic stem cells	blood
38	chr12:104871600-104872600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
39	chr12:104871600-104872600	Flanking Active TSS	Fetal Thymus	thymus
40	chr12:104871600-104872800	Flanking Active TSS	Primary B cells from peripheral blood	blood
41	chr12:104871600-104872800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
42	chr12:104871600-104872800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr12:104871600-104873000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr12:104871600-104873000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr12:104871600-104873000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr12:104871600-104874000	Flanking Active TSS	K562	blood
47	chr12:104871800-104872400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
48	chr12:104871800-104872400	Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr12:104871800-104872600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
50	chr12:104871800-104872600	Enhancers	Adipose Nuclei	Adipose

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