Variant report

Variant	rs2004295
Chromosome Location	chr6:39154866-39154867
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:39152659..39161573-chr6:39191951..39198831,12	K562	blood:
2	chr6:39146393..39149644-chr6:39153708..39157375,4	K562	blood:
3	chr6:39146675..39149644-chr6:39153708..39155552,2	K562	blood:
4	chr6:39154173..39155788-chr6:39270095..39272270,2	K562	blood:
5	chr6:39154121..39155675-chr6:39156063..39158781,2	K562	blood:
6	chr6:39153346..39156056-chr6:39270382..39273616,3	K562	blood:
7	chr6:39139089..39141843-chr6:39153750..39157319,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164626	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1155349	0.82[JPT][hapmap]
rs2815095	0.86[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34790217	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs724650	0.86[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs733701	0.82[JPT][hapmap]
rs9394578	0.82[JPT][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	nsv1028088	chr6:38821047-39163549	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS 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	10 gene(s)	inside rSNPs	diseases
2	nsv538205	chr6:38821047-39163549	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv830644	chr6:39116530-39325980	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1022974	chr6:39120271-39277553	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2004295	PIM1	cis	parietal	SCAN
rs2004295	PI16	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39139600-39157600	Weak transcription	Ovary	ovary
2	chr6:39146200-39160400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:39146600-39157400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr6:39147400-39156000	Weak transcription	Small Intestine	intestine
5	chr6:39148600-39157000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:39149000-39168000	Weak transcription	Fetal Kidney	kidney
7	chr6:39150000-39158800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr6:39150200-39155200	Weak transcription	Fetal Thymus	thymus
9	chr6:39150200-39157600	Weak transcription	Spleen	Spleen
10	chr6:39150600-39193800	Genic enhancers	Fetal Intestine Small	intestine
11	chr6:39150800-39156200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr6:39150800-39158400	Enhancers	Stomach Mucosa	stomach
13	chr6:39151000-39156600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:39151000-39157200	Enhancers	Duodenum Mucosa	Duodenum
15	chr6:39151000-39165200	Strong transcription	H9 Cell Line	embryonic stem cell
16	chr6:39151200-39155800	Enhancers	Rectal Mucosa Donor 29	rectum
17	chr6:39151200-39156200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:39151200-39156200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr6:39151200-39156800	Enhancers	Colonic Mucosa	Colon
20	chr6:39151400-39162200	Weak transcription	Thymus	Thymus
21	chr6:39151600-39161000	Strong transcription	Fetal Stomach	stomach
22	chr6:39151800-39155200	Weak transcription	Lung	lung
23	chr6:39152200-39155400	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr6:39152800-39156200	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr6:39153000-39156000	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr6:39153200-39156000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr6:39153200-39162000	Genic enhancers	Placenta	Placenta
28	chr6:39153400-39155200	Weak transcription	Pancreas	Pancrea
29	chr6:39153400-39157600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr6:39153400-39158000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr6:39153600-39155600	Weak transcription	A549	lung
32	chr6:39153800-39156400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr6:39154000-39157600	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr6:39154000-39157600	Strong transcription	Liver	Liver
35	chr6:39154200-39157200	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr6:39154200-39159800	Enhancers	Fetal Muscle Trunk	muscle
37	chr6:39154200-39164200	Genic enhancers	Fetal Intestine Large	intestine
38	chr6:39154400-39155400	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr6:39154400-39156800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr6:39154400-39162400	Weak transcription	Hela-S3	cervix
41	chr6:39154400-39164400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr6:39154600-39155000	Weak transcription	Esophagus	oesophagus
43	chr6:39154600-39155000	Enhancers	Gastric	stomach
44	chr6:39154800-39155200	Enhancers	K562	blood
45	chr6:39154800-39155600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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