Variant report

Variant	rs34495920
Chromosome Location	chr1:70813586-70813587
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:70812176..70814577-chr1:70818800..70821744,3	MCF-7	breast:
2	chr1:70809714..70814478-chr1:70818976..70822377,5	MCF-7	breast:
3	chr1:70812176..70814908-chr1:70864607..70866509,2	K562	blood:

Variant related genes	Relation type
ENSG00000197568	Chromatin interaction
ENSG00000118454	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12139863	0.85[CEU][hapmap]
rs12563524	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12565719	0.93[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs61216997	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999219	chr1:70730556-71014911	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	nsv1012563	chr1:70753332-70832118	Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	esv1792702	chr1:70755511-70818576	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv1801665	chr1:70755511-70832053	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	nsv871430	chr1:70765659-70819912	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv830137	chr1:70765921-70958718	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs34495920	HHLA3	cis	lymphoblastoid	seeQTL
rs34495920	HHLA3	cis	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70688000-70819200	Weak transcription	Esophagus	oesophagus
2	chr1:70716800-70815800	Weak transcription	Brain Angular Gyrus	brain
3	chr1:70760600-70818200	Weak transcription	Aorta	Aorta
4	chr1:70760600-70818600	Weak transcription	Thymus	Thymus
5	chr1:70762000-70817600	Weak transcription	NHLF	lung
6	chr1:70762200-70818200	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr1:70765600-70818200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr1:70767800-70819000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:70768200-70817000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr1:70770400-70817200	Weak transcription	Pancreas	Pancrea
11	chr1:70773600-70818200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr1:70773800-70818200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:70774200-70815200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:70774200-70818000	Weak transcription	Fetal Kidney	kidney
15	chr1:70784200-70817400	Weak transcription	Small Intestine	intestine
16	chr1:70787400-70817600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr1:70788600-70818200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:70789000-70816000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr1:70789200-70818200	Weak transcription	Right Atrium	heart
20	chr1:70790600-70815400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:70790600-70816400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr1:70790600-70818000	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:70790600-70818400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr1:70793600-70818000	Weak transcription	NH-A	brain
25	chr1:70794400-70818000	Weak transcription	HMEC	breast
26	chr1:70797800-70815800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:70798000-70815000	Weak transcription	NHEK	skin
28	chr1:70798000-70816400	Weak transcription	Brain Anterior Caudate	brain
29	chr1:70799400-70815000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:70799400-70818000	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr1:70799600-70817600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr1:70799600-70818000	Weak transcription	K562	blood
33	chr1:70799600-70818600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr1:70800000-70814400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:70800400-70814400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:70800400-70815000	Weak transcription	HepG2	liver
37	chr1:70800400-70815200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr1:70800400-70816400	Weak transcription	Fetal Lung	lung
39	chr1:70800400-70817000	Weak transcription	Adipose Nuclei	Adipose
40	chr1:70800400-70817600	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr1:70800400-70817600	Weak transcription	NHDF-Ad	bronchial
42	chr1:70800400-70818200	Weak transcription	Primary B cells from cord blood	blood
43	chr1:70800400-70818200	Weak transcription	HSMM	muscle
44	chr1:70800400-70818400	Weak transcription	Fetal Intestine Large	intestine
45	chr1:70800400-70819200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr1:70800400-70819200	Weak transcription	Placenta	Placenta
47	chr1:70800600-70815400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:70800600-70817200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr1:70801000-70814600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:70801000-70817600	Weak transcription	Duodenum Mucosa	Duodenum

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