Variant report

Variant	rs6419387
Chromosome Location	chr12:104864883-104864884
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104861083..104865275-chr12:104866418..104870159,5	K562	blood:
2	chr12:104852839..104855254-chr12:104863893..104866118,2	K562	blood:
3	chr12:104858578..104860832-chr12:104863067..104865005,3	K562	blood:
4	chr12:104850865..104852398-chr12:104863309..104864984,2	MCF-7	breast:

Extended variants
information (count: 5 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs4964797	0.88[CEU][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6419387	GNPTAB	cis	parietal	SCAN
rs6419387	PMCH	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104853200-104868600	Weak transcription	Fetal Muscle Trunk	muscle
2	chr12:104853600-104867000	Enhancers	Primary B cells from peripheral blood	blood
3	chr12:104853800-104870600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr12:104854200-104867600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:104855200-104868200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr12:104855200-104868600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:104855400-104866400	Weak transcription	Brain Germinal Matrix	brain
8	chr12:104855400-104874400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:104855400-104874800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:104856800-104867400	Enhancers	Thymus	Thymus
11	chr12:104857000-104865600	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr12:104857000-104867000	Weak transcription	NH-A	brain
13	chr12:104857000-104868200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:104857000-104873600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:104857200-104869200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr12:104857400-104866200	Weak transcription	Fetal Stomach	stomach
17	chr12:104857600-104869200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr12:104857800-104867000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr12:104857800-104867000	Weak transcription	Left Ventricle	heart
20	chr12:104857800-104867000	Weak transcription	HUVEC	blood vessel
21	chr12:104857800-104871800	Weak transcription	Right Atrium	heart
22	chr12:104857800-104873600	Weak transcription	A549	lung
23	chr12:104858200-104866600	Weak transcription	Placenta	Placenta
24	chr12:104859200-104867200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr12:104859200-104879800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr12:104859400-104866600	Weak transcription	Colonic Mucosa	Colon
27	chr12:104861400-104866600	Weak transcription	Small Intestine	intestine
28	chr12:104861600-104866400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr12:104861800-104867000	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr12:104861800-104869200	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr12:104862200-104865000	ZNF genes & repeats	GM12878-XiMat	blood
32	chr12:104862600-104866600	Weak transcription	Gastric	stomach
33	chr12:104862600-104867400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr12:104862800-104866800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr12:104863000-104865400	Transcr. at gene 5' and 3'	Dnd41	blood
36	chr12:104863200-104866400	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr12:104863200-104866400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr12:104863200-104866400	Weak transcription	Lung	lung
39	chr12:104863400-104866400	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr12:104863400-104866400	Weak transcription	Brain Anterior Caudate	brain
41	chr12:104863400-104866400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr12:104863400-104869600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr12:104863400-104879200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr12:104863600-104865200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr12:104863600-104866200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr12:104863600-104866200	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr12:104863600-104866400	Weak transcription	Duodenum Mucosa	Duodenum
48	chr12:104863600-104867000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr12:104863600-104867200	Weak transcription	Fetal Brain Female	brain
50	chr12:104863800-104866600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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